Factor viii mutation repair and tolerance induction

ABSTRACT

Methods of treating hemophilia A in a subject with an F8 gene mutation, wherein the F8 gene is repaired and the resultant repaired gene, upon expression, confers improved coagulation functionality to the encoded FVIII protein of the subject compared to the non-repaired F8 gene. The invention also includes methods of inducing immune tolerance to a FVIII replacement product ((r)FVIII) in a subject having a FVIII deficiency, wherein the F8 gene mutation is repaired and the repaired gene, upon expression, provides for the induction of immune tolerance to an administered replacement FVIII protein product. The invention also includes isolated nucleic acids, vectors, recombinant viruses, cells, and pharmaceutical compositions to repair the F8 gene.

STATEMENT OF RELATED APPLICATIONS

This application claims priority from Provisional U.S. Application No. 61/734,678 filed Dec. 7, 2012, and Provisional U.S. Application No. 61/888,424 filed Oct. 8, 2013. The entirety of each of these applications is hereby incorporated by reference for all purposes.

GOVERNMENT INTEREST

The U.S. Government has rights in this invention by virtue of support under Grant No. RC2 HL101851 awarded by the National Institute of Health and the National Heart, Lung, and Blood Institute.

STATEMENT REGARDING SEQUENCE LISTING

The Sequence Listing associated with this application is provided in text format in lieu of a paper copy, and is hereby incorporated by reference into the specification. The name of the text file containing the Sequence Listing is 22002-007WO1_Sequencelisting_patentin_ST25.txt. The text file is 109 kb, was created on Dec. 6, 2013, and is being submitted electronically via EFS-Web.

BACKGROUND

Hemophilia (HA) is caused by loss-of-function mutations in the X-linked Factor (F) VIII gene, F8. Infusion of replacement plasma-derived (pd) or recombinant (r) FVIII is the standard of care to manage this chronic disease. Infusion of replacement FVIII, however, is not a cure for HA. Spontaneous bleeding remains a serious problem especially for those with severe HA, defined as circulating levels of FVIII coagulant activity (FVIII: C) below 1% of normal. Furthermore, the formation of anti-FVIII antibodies occurs in about 20% of all patients and more often in certain subpopulations of HA patients, such as African Americans (Viel K R, Ameri A, Abshire T C, et al. Inhibitors of factor VIII in black patients with hemophilia. N Engl J Med. 360: 1618-27, 2009). Patients unable to be treated with FVIII experience more painful, joint bleeding and over time, a greater loss of mobility than patients whose HA is able to be managed with FVIII.

The approval in Europe of the first gene therapy obtained by uniQuire BV for alipogenic tiparvovec (trade name Glybera) to treat lipoprotein lipase (LPL) deficiency is a milestone in the quest to bring gene-based therapeutics into clinical use. Tiparvovec (AAV1-LPL(S447X)) incorporates an intact human LPL gene (LPL) variant, i.e. LPL(Ser447X), in an adeno-associated virus (AAV) vector, which is delivered intramuscularly (Gaudet D, Méthot J, Déry S, et al. Efficacy and long-term safety of alipogene tiparvovec (AAV1LPL(S447X)) gene therapy for lipoprotein lipase deficiency: an open-label trial. Gene Ther. Jun. 21, 2012. [Epub ahead of print]). The benefits of restoring continuous circulation of clinically meaningful levels of FVIII has motivated intense efforts over decades to develop an effective gene therapy for hemophilia. Use of an AAV vector to deliver the gene that encodes FIX is bearing fruit in the treatment of hemophilia B (HB) (Nathwani A, Tuddenham E G D, Rangarjan S, et al. Adeno-associated viral vector mediated gene transfer for hemophilia B. Blood. 118(21): 4-5, 2011). HB in six adult patients has been converted from a severe form to mild or moderate HB, following intravenous infusion of an AAV8 vector incorporating human F9 under the control of a liver restricted promoter (High K A. The gene therapy journey for hemophilia: are we there yet? Blood. 120(23): 4482-7, 2012). These patients have maintained a circulating FIX coagulant activity (FIX: C) level ranging from 1-6% of normal for 3 years.

Although very encouraging, the AAV vector is not suitable for many HB patients and safety concerns remain. AAV vectors have been engineered from a wild-type parvovirus capable of naturally infecting humans (Calcedo R, Morizono H, Wang L, et al. Adeno-associated virus antibody profiles in newborns, children, and adolescents. Clin Vaccine Immunol. 18(9): 1586-8, 2011; High K A. The gene therapy journey for hemophilia: are we there yet? Blood. 120(23): 4482-7, 2012). In the current AAV trial, patients are screened for neutralizing antibodies against AAV. Thus, about 30-50% of hemophilia patients may not be eligible for this treatment (High K A. The gene therapy journey for hemophilia: are we there yet? Blood. 120(23): 4482-7, 2012). Patients with liver disease are also not eligible for this therapy pending a better understanding of safety. Furthermore, because the vectors are predominantly non-integrating, they are not suitable for use with young patients because expression of FIX would be expected to be lost as the patient grows (High K A. The gene therapy journey for hemophilia: are we there yet? Blood. 120(23): 4482-7, 2012).

Transmission of AAV to the germ-line (semen) has been reported, but this appears to be transient (High K A. The gene therapy journey for hemophilia: are we there yet? Blood. 120(23): 4482-7, 2012). There is a trend toward a dose-dependent memory T-cell mediated response to AAV. This was seen in the first HB trial done with AAV and again in the current trial for HB (High K A. The gene therapy journey for hemophilia: are we there yet? Blood.

120(23): 4482-7, 2012). Whereas dosing in four patients in the range of 2×10¹¹ vg/kg did not provoke a T-cell response, it provided only low circulating FIX: C levels (1-3%). Dosing at 2×10¹² vg/kg in two patients led to initial robust levels of FIX in circulation, 8-10%; but, at 8-weeks post infusion, FIX levels began to fall and patients' liver enzymes rose (High K A. The gene therapy journey for hemophilia: are we there yet? Blood. 120(23): 4482-7, 2012). Treatment with prednisolone was effective in restoring normal liver enzyme levels and reducing AAV-capsid specific T-cells within PBMCs (High K A. The gene therapy journey for hemophilia: are we there yet? Blood. 120(23): 4482-7, 2012). In one patient, FIX fell to 2% of normal, but the other maintained FIX levels at 6% of normal (High K A. The gene therapy journey for hemophilia: are we there yet? Blood. 120(23): 4482-7, 2012). Questions remain about the long-term safety of therapy with AAV. Sequencing studies of organs from animals treated with AAV demonstrate that integration of AAV occurs (Naki H, Yant S R, Storm T A, Fuess S, Meuse L, Kay M S. Extrachromosomal recombinant adenoassociated virus vector genomes are primarily responsible for stable liver transduction in vivo. J Virol. 75(15): 6969-76, 2001). There is also one report of neonatal mice injected with AAV2 experiencing an increase in hepatocellular carcinoma with some tumors containing vector DNA (Chuah M K, Nair N, VandenDriessche T. Recent progress in gene therapy for hemophilia. Hum Gene Ther. 23(6): 557-65, 2012). Whether AAV will prove to have any utility for delivering F8 to HA patients is an open question. The cloning capacity of the vector is limited to replacement of the virus' 4.8 kilobase genome. Promising preclinical results have been obtained using an AAV packaged, non-naturally occurring F8 cDNA, encoding B-domain-deleted (BDD)-rFVIII. One major caveat is that the dosing required to achieve desired levels of circulating FVIII (1-7.8%) in these studies was a log higher than the highest dose used in the current HB trial (Chuah M K, Nair N, VandenDriessche T. Recent progress in gene therapy for hemophilia. Hum Gene Ther. 23(6): 557-65, 2012; Jonathan D. Finn, Margareth C. Eradictaion of neutralizing antibodies to FVIII in canine hemophilia A after liver gene therapy. Blood 116: 5842-5848 2010). Experience in the HB trial suggests that a memory T-cell response targeting liver cells would occur at these doses (High K A. The gene therapy journey for hemophilia: are we there yet? Blood. 120(23): 4482-7, 2012; Chuah M K, Nair N, VandenDriessche T. Recent progress in gene therapy for hemophilia. Hum Gene Ther. 23(6): 557-65, 2012).

A substantial effort has been made to develop lentiviral vectors for the delivery of clotting factors (Chuah M K, Nair N, VandenDriessche T. Recent progress in gene therapy for hemophilia. Hum Gene Ther. 23(6): 557-65, 2012). Lentiviral vectors can transfect non-cycling hepatocytes and integrate into the host genome. While the latter attribute may afford long term expression of the factor, it raises serious safety concerns regarding insertional mutagenesis leading to activation of oncogenes or inactivation of repressors. Studies in an HB mouse indicate that a preferred lentiviral vector could be one that harbors an inactivation mutation of the integrase, termed an IDLV (integrase defective lentiviral viral vector) (Matria J, Chuah M K, VandenDriessche T. Recent advances in lentiviral vector development and applications. Mol Ther. 18: 477-90, 2010). Although factor expression is diminished following the elimination of integration, it appears this may be offset in the case of FIX by use of a rare hyper-activating variant in a codon-optimized F9 cDNA which dramatically boosts circulating FIX levels (Matria J, Chuah M K, VandenDriessche T. Recent advances in lentiviral vector development and applications. Mol Ther. 18: 477-90, 2010). Another obstacle with lentivirus is its competence to transfect APCs which triggers deleterious T-cell mediated immune responses that can neutralize the secreted clotting factor; or eliminate the transduced hepatocytes (VandenDriessche T, Thorerezn L, Naldini L, et al. Lentiviral vectors containing the human immunodeficiency virus type-1 central polypurine track can efficiently transduce non-dividing hepatocytes and antigen presenting cells in vivo. Blood. 100: 813-22, 2002). This can be reduced in animal models by including an additional layer of post-transcriptional control, mediated by the use of endogenous microRNA (miR) (Matria J, Chuah M K, VandenDriessche T. Recent advances in lentiviral vector development and applications. Mol Ther. 18: 477-90, 2010). Whether manipulations designed to mute the immune response to lentivirus will translate to man is unknown. In contrast to what occurs in man, in the canine model, AAV vectors did not elicit an immune response. Hence, while animal models have proven predictive with regard to forecasting delivery of factor clotting activity; no animal model, including the canine, recapitulates the more refined and sophisticated human immune response.

Use of autologous cells engineered with viral elements or nucleases capable of genomic editing may permit greater safety than intravenous delivery of targeted virus. Ex vivo protocols allow for screening of the genomes of manipulated cells to assess the frequency or viral insertions, double strand breaks in DNA (DSBs) or other potentially mutagenic events (Li H, Haurigot V, Doyon Y, et al. In vivo genome editing restores haemostasis in a mouse model of haemophilia. Nature. 475(7355): 217-21, 2011). Levels of blood clotting proteins needed to maintain hemostasis may be more readily achieved by expansion of large populations of cells ex vivo and reintroduction(s) into the patient. Promising work has been done with murine hematopoietic stem cells (HSCs) transduced with lentivirus to express FVIII, including in HA mice with high-titer FVIII inhibitors (Calcedo R, Morizono H, Wang L, et al. Adeno-associated virus antibody profiles in newborns, children, and adolescents. Clin Vaccine Immunol. 18(9): 1586-8, 2011; Chuah M K, Nair N, VandenDriessche T. Recent progress in gene therapy for hemophilia. Hum Gene Ther. 23(6): 557-65, 2012). Enthusiasm for these approaches is tempered, however, by recognition that in order to promote engraftment, conditioning agents such as busulfan, which can have serious side effects are required (Chuah M K, Nair N, VandenDriessche T. Recent progress in gene therapy for hemophilia. Hum Gene Ther. 23(6): 557-65, 2012). Furthermore, concerns remain regarding the long-term consequences of lentiviral incorporation into the genomes of hematopoietic stem cells (HSCs).

In addition, there is a critical need to identify ways to avoid FVIII inhibitor development and to abate a FVIII inhibitor response. An arduous (frequent infusions of FVIII) and extremely expensive (˜$1 MM/patient) protocol called Immune Tolerance Induction (ITI) is the only approach proven to eradicate FVIII inhibitors in HA patients, yet fails among 30% of inhibitor patients (Morfin M. et. al. European study on orthopaedic status of haemophilia patients with inhibitors. Haemophiia Sep; 13(5):606-12 2007). Twenty percent of HA patients with the F8I22I develop inhibitors. In addition, HA patients with missense mutations expressed in the C2 domain of FVIII are more prone to inhibitor formation than those with mutations expressed elsewhere in their endogenous FVIII (8.7% C1/C2 domain vs. 3.6% non-C1/C2-domain; p-value: 0.01 sample size 1135 HA patients).

SUMMARY

The invention includes a method of treating a human subject with hemophilia A comprising selectively targeting and replacing a portion of the subject's genomic F8 gene sequence containing a mutation in the gene with a replacement sequence. In one embodiment, the resultant repaired gene, upon expression, confers improved coagulation functionality to the encoded FVIII protein of the subject compared to the non-repaired F8 gene. In one embodiment, the repaired gene, upon expression, provides for the induction of immune tolerance to an administered replacement FVIII protein product.

In one aspect of the invention, a method of treating hemophilia A in a subject is provided comprising introducing into a cell of the subject one or more isolated nucleic acids encoding a nuclease that targets a portion of the F8 gene containing a mutation that causes hemophilia A, wherein the nuclease creates a double stranded break in the F8 gene; and an isolated nucleic acid comprising a donor sequence comprising (i) a nucleic acid encoding a truncated FVIII polypeptide or (ii) a native F8 3′ splice acceptor site operably linked to a nucleic acid encoding a truncated FVIII polypeptide, wherein the nucleic acid comprising the (i) a nucleic acid encoding a truncated FVIII polypeptide or (ii) native F8 3′ splice acceptor site operably linked to a nucleic acid encoding a truncated FVIII polypeptide is flanked by nucleic acid sequences homologous to the nucleic acid sequences upstream and downstream of the double stranded break in the DNA, and wherein the resultant repaired gene, upon expression, confers improved coagulation functionality to the encoded FVIII protein of the subject compared to the non-repaired F8 gene. In one particular embodiment, the donor sequence comprises a native F8 3′ splice acceptor site operably linked to a nucleic acid encoding a truncated FVIII polypeptide. In one embodiment, the subject is a human. In one embodiment, the nucleic acids encoding the nuclease introduced into the cell are ribonucleic acids.

In one aspect, the invention provides a method of inducing immune tolerance to a FVIII replacement product ((r)FVIII) in a subject having a FVIII deficiency and who will be administered, is being administered, or has been administered a (r)FVIII product comprising introducing into a cell of the subject one or more nucleic acids encoding a nuclease that targets a portion of the F8 gene containing a mutation that causes hemophilia A, wherein the nuclease creates a double stranded break in the F8 gene; and an isolated nucleic acid comprising a donor sequence comprising a(i) a nucleic acid encoding a truncated FVIII polypeptide or (ii) a native F8 3′ splice acceptor site operably linked to a nucleic acid encoding a truncated FVIII polypeptide, wherein the nucleic acid comprising the (i) a nucleic acid encoding a truncated FVIII polypeptide or (ii) native F8 3′ splice acceptor site operably linked to a nucleic acid encoding a truncated FVIII polypeptide is flanked by nucleic acid sequences homologous to the nucleic acid sequences upstream and downstream of the double stranded break in the DNA, and wherein the repaired gene, upon expression, provides for the induction of immune tolerance to an administered replacement FVIII protein product. In one particular embodiment, the donor sequence comprises a native F8 3′ splice acceptor site operably linked to a nucleic acid encoding a truncated FVIII polypeptide. In one embodiment, the truncated FVIII polypeptide amino acid sequence shares homology with a positionally coordinated portion of the (r)FVIII amino acid sequence. In one embodiment, the truncated FVIII polypeptide amino acid sequence shares complete homology with a positionally correlated portion of the (r)FVIII amino acid sequence. In one embodiment, the subject is a human. In one embodiment, the nucleic acids encoding the nuclease introduced into the cell are ribonucleic acids.

In one embodiment, the F8 mutation targeted for replacement is a point mutation, a deletion, or an inversion. In one embodiment of the above described aspects, the nuclease targets the F8 gene at intron 1. In one embodiment, the nuclease targets a F8 gene at intron 14. In one embodiment, the nuclease targets the F8 gene at intron 22. In a particular embodiment, the mutation targeted for repair is an intron 22 inversion (I22I).

In one embodiment of the above described aspects, the nuclease targets the F8 gene at exonl/intron 1 junction, exon14/intron 14 junction, or exon22/intron 22 junction.

In one embodiment of the above described aspects, the encoded nuclease is a zinc finger nuclease (ZFN). In one embodiment, the encoded nuclease is a Transcription Activator-Like Effector Nuclease (TALEN). In one embodiment, the encoded nuclease is a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-associated (Cas) nuclease. In one particular embodiment, the encoded nuclease is a TALEN.

In the methods provided herein, the nucleic acids can optionally be in a vector.

In one embodiment of the above described aspects, the isolated nucleic acids described above can be administered directly to the subject so that introduction into the subject's cell occurs in vivo.

The isolated nucleic acids can be delivered to the subject's cells in vivo by a variety of mechanisms, including through uptake of naked DNA, liposome fusion, or through viral transduction, for example adenovirus, adeno-associated virus (AAV), or lentivirus introduction, as described further below.

In one embodiment of the above described aspects, the isolated nucleic acids described above can be administered ex vivo to a cell that has been isolated from the subject. The isolated nucleic acids can be delivered to the cells via any gene transfer mechanism, for example, calcium phosphate mediated gene delivery, electroporation, microinjection, liposome delivery, endocytosis, or viral delivery, for example, adenoviral, AAV, or lentiviral delivery, as described further below. The transduced cells can then be infused (e.g., in a pharmaceutically acceptable carrier) or homotopically transplanted back into the subject per standard methods for the cell or tissue type. Standard methods are known for transplantation or infusion of various cells into a subject. In one embodiment, the nucleic acids encoding the nuclease can be introduced into the cell as ribonucleic acids, for example mRNA. Alternatively, the nucleic acids can optionally be in a DNA vector.

In one embodiment of the above described aspects, the cells are endothelial cells. In one embodiment, the endothelial cell is a blood outgrowth endothelial cells (BOECs). In one embodiment, the cells repaired reside within the liver. In one embodiment, the cells are hepatocytes. In one embodiment, the cells are liver sinusoidal endothelial cells (LESCs). In one embodiment, the cells are stem cells. In one embodiment, the stem cells are induced pluripotent stem cells (iPSCs).

In one embodiment of the above described aspects, the nucleic acids described above are introduced into blood outgrowth endothelial cells (BOECs) that have been co-cultured with additional cell types. In one embodiment, the cells are blood outgrowth endothelial cells (BOECs) that have been co-cultured with hepatocytes or liver sinusoidal endothelial cell (LESCs), or both. In one embodiment, the cells are blood outgrowth endothelial cells (BOECs) that have been co-cultured with induced pluripotent stem cells (iPSCs).

Cells comprising the nucleic acids set forth herein are further provided. These cells can be, for example, endothelial cells, LSECs, BOECs, stem cells, for example iPSCs, or hepatocytes.

Recombinant viruses comprising any of the nucleic acids set forth herein are also provided.

Pharmaceutical compositions comprising any of the nucleic acids, vectors comprising the nucleic acids, recombinant viruses comprising the nucleic acids, or cells comprising the nucleic acids described herein are also provided. These pharmaceutical compositions can be in a pharmaceutically acceptable carrier.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is schematic illustration of the wild-type and intron-22-inverted FVIII loci (F8 & F8_(I22I)) and their expressed protein products (FVIII_(FL) & FVIII_(B) for F8 and FVIII_(I22I) & FVIII_(B) for F8_(I22I)).

FIG. 2 is a schematic illustration of a TALEN-mediated genomic editing that can be used to repair the human intron-22 (I22)-inverted F8 locus, F8_(I22I).

FIG. 3 shows a functional heterodimeric TALEN, comprised of its left and right monomer subunits (TALEN-L and TALEN-R), targeting the human F8 gene.

FIG. 4 shows a functional heterodimeric TALEN, comprised of its left and right monomer subunits (TALEN-L and TALEN-R) targeting the canine F8 gene

FIG. 5 illustrates the TALEN approach linking Exon 22 of the F8 gene to a nucleic acid encoding a truncated FVIII polypeptide encoding exons 23-26.

FIG. 6 illustrates the TALEN approach linking Intron 22 to a F8 3′ splice acceptor site operably linked to a nucleic acid encoding a truncated FVIII polypeptide.

FIG. 7 shows a comparison of expected genomic DNA, spliced RNA and proteins pre and post repair.

FIG. 8 shows PCR primer design to confirm correct integration of exons 23-26 to repair the human intron-22 (I22)-inverted F8 locus, F8_(I22I).

FIG. 9 illustrates the donor plasmid targeting the F8 Exon22/Intron22 junction using a TALEN nuclease, zinc finger nuclease, or cas nuclease approach.

FIG. 10 illustrates the donor plasmid targeting the F8 Exon1/Intron1 junction using a TALEN nuclease, zinc finger nuclease, or cas nuclease approach.

FIG. 11 illustrates the donor plasmid targeting the F8 Intron 22 region using a TALEN nuclease, zinc finger nuclease, or cas nuclease approach.

FIG. 12 illustrates the donor plasmid targeting the F8 Intron 1 region using a TALEN nuclease, zinc finger nuclease, or cas nuclease approach.

FIG. 13 illustrates the CRISPR/Cas9-mediated F8 repair strategy targeting intron 1.

DETAILED DESCRIPTION

The invention includes a method of treating a subject with hemophilia A comprising selectively targeting and replacing a portion of the subject's genomic F8 gene sequence containing a mutation in the gene with a replacement sequence. In one embodiment, the resultant repaired gene containing the replacement sequence, upon expression, confers improved coagulation functionality to the encoded FVIII protein of the subject compared to the non-repaired F8 gene. Preferably, the levels of functional FVIII in circulation are adequate to obviate or reduce the need for infusions of replacement FVIII in the subject. In one embodiment, expression of functional FVIII reduces whole blood clotting time (WBCT). In one embodiment, the repaired gene, upon expression, provides for the induction of immune tolerance to an administered replacement FVIII protein product. In one embodiment, the subject is a human.

In one aspect of the invention, a method of treating hemophilia A in a subject is provided comprising introducing into a cell of the subject one or more nucleic acids encoding a nuclease that targets a portion of the human F8 gene containing a mutation that causes hemophilia A, wherein the nuclease creates a double stranded break in the F8 gene; and an isolated nucleic acid comprising (i) a nucleic acid encoding a truncated FVIII polypeptide or (ii) a native F8 3′ splice acceptor site operably linked to a nucleic acid encoding a truncated FVIII polypeptide, wherein the nucleic acid comprising the (i) a nucleic acid encoding a truncated FVIII polypeptide or (ii) native F8 3′ splice acceptor site operably linked to a nucleic acid encoding a truncated FVIII polypeptide is flanked by nucleic acid sequences homologous to the nucleic acid sequences upstream and downstream of the double stranded break in the DNA, and wherein the resultant repaired gene, upon expression, confers improved coagulation functionality to the encoded FVIII protein of the subject compared to the non-repaired F8 gene.

In one aspect, the invention is a method of inducing immune tolerance to a FVIII replacement product (r)FVIII in a subject having a FVIII deficiency and who will be administered, is being administered, or has been administered a (r)FVIII product comprising introducing into a cell of the subject one or more nucleic acids encoding a nuclease that targets a portion of the F8 gene containing a mutation that causes hemophilia A, wherein the nuclease creates a double stranded break in the F8 gene; and an isolated nucleic acid comprising (i) a nucleic acid encoding a truncated FVIII polypeptide or (ii) a native F8 3′ splice acceptor site operably linked to a nucleic acid encoding a truncated FVIII polypeptide, wherein the nucleic acid comprising the (i) a nucleic acid encoding a truncated FVIII polypeptide or (ii) native F8 3′ splice acceptor site operably linked to a nucleic acid encoding a truncated FVIII polypeptide is flanked by nucleic acid sequences homologous to the nucleic acid sequences upstream and downstream of the double stranded break in the DNA, and wherein the repaired gene, upon expression, provides for the induction of immune tolerance to an administered replacement FVIII protein product. The person administered the cells may have no anti-FVIII antibodies or have anti-FVIII antibodies as detected by ELISA or Bethesda assays. In one embodiment, the truncated FVIII polypeptide amino acid sequence shares homology with a portion of the (r)FVIII amino acid sequence. In one embodiment, the truncated FVIII polypeptide amino acid sequence shares homology with a similar portion of the (r)FVIII amino acid sequence. In one embodiment, the truncated FVIII polypeptide amino acid sequence shares complete homology with a similar portion of the (r)FVIII amino acid sequence.

1. Definitions

The terms “nucleic acid,” “polynucleotide,” and “oligonucleotide” are used interchangeably and refer to a deoxyribonucleotide or ribonucleotide polymer, in linear or circular conformation, and in either single- or double-stranded form. For the purposes of the present disclosure, these terms are not to be construed as limiting with respect to the length of a polymer. The terms can encompass known analogues of natural nucleotides, as well as nucleotides that are modified in the base, sugar and/or phosphate moieties (e.g., phosphorothioate backbones). In general, an analogue of a particular nucleotide has the same base-pairing specificity; i.e., an analogue of A will base-pair with T.

The terms “polypeptide,” “peptide,” and “protein” are used interchangeably to refer to a polymer of amino acid residues. The term also applies to amino acid polymers in which one or more amino acids are chemical analogues or modified derivatives of a corresponding naturally-occurring amino acids. As used throughout, by subject is meant an individual. Preferably, the subject is a mammal such as a primate, and, more preferably, a human. Non-human primates are subjects as well. The term subject includes domesticated animals, such as cats, dogs, etc., livestock (for example, cattle, horses, pigs, sheep, goats, etc.) and laboratory animals (for example, ferret, chinchilla, mouse, rabbit, rat, gerbil, guinea pig, etc.). Thus, veterinary uses and medical formulations are contemplated herein.

The term “truncated FVIII polypeptide” refers to an amino acid sequence that contains less than the full length FVIII protein. The truncated FVIII polypeptide can be truncated from the 5′ end of the amino acid sequence. This produces an amino acid sequence corresponding to a portion of the FVIII protein, where a variable amount of the amino acid sequence is missing from the 5′ end of the protein. In one embodiment, the truncated FVIII polypeptide contains exons 23-26. In one embodiment, the truncated FVIII polypeptide contains exons 2-26. In one embodiment, the truncated FVIII polypeptide contains exons 15-26.

2. F8 Gene Mutations

The F8 gene, located on the X chromosome, encodes a coagulation factor (Factor VIII) involved in the coagulation cascade that leads to clotting. Factor VIII is chiefly made by cells in the liver, and circulates in the bloodstream in an inactive form, bound to von Willebrand factor. Upon injury, FVIII is activated. The activated protein (FVIIIa) interacts with coagulation factor IX, leading to clotting.

Mutations in the F8 gene cause hemophilia A (HA). Over 2100 mutations in the gene have been identified, including point mutations, deletions, and insertion. One of the most common mutations includes inversion of intron 22, which leads to a severe type of HA. Mutations in F8 can lead to the production of an abnormally functioning FVIII protein or a reduced or absent amount of circulating FVIII protein, leading to the reduction of or absence of the ability to clot in response to injury.

In one aspect, the present invention is directed to the targeting and repair of F8 gene mutations in a subject suffering from hemophilia A using the methods described herein. Approximately 98% of patients with a diagnosis of hemophilia A are found to have a mutation in the F8 gene (i.e., intron 1 and 22 inversions, point mutations, insertions, and deletions).

Identification of an HA subject's mutation for targeting and repair can be readily made by using techniques known in the art. For example, DNA from the subject can be extracted from leukocytes in whole blood and all the endogenous coding regions and splice junctions of the F8 gene can be analyzed by restriction analysis, direct DNA sequence analysis, Denaturing Gradient Gel Electrophoresis (DGGE), Chemical Mismatch Cleavage (CMC), and Denaturing High Performance Liquid Chromatography (DHPLC) (see, for example: Higuchi et al., Characterization of mutations in the factor VIII gene by direct sequencing of amplified genomic DNA. Genomics 1990: 6(1); 65-71, Schwaab et al. Mutations in hemophilia A. Br J Haematol 1993; 83: 450-458; Schwaab et al. Factor VIII gene mutations found by a comparative study of SSCP, DGGE, and CMC and their analysis on a molecular model of factor VIII protein. Hum Genet 1997; 101: 323-332; Oldenburg et al. Evaluation of DHPLC in the analysis of hemophilia A. J Biochem Biophys Methods 2001; 47: 39-51). Intron 22 inversions account for approximately 45% and intron 1 inversions account for approximately 2% to 3%, of mutations associated with severe hemophilia A. The identification of inversions is well known in the art (see, for example, Viel at al. Inhibitors of Factor VIII in Black Patients with Hemophilia. N Engl J Med 2009; 360(16): 1618-1627).

In one embodiment of the present invention, the gene mutation targeted for repair is a point mutation. In one embodiment, the gene mutation targeted for repair is a deletion. In one embodiment, the gene mutation targeted for repair is an inversion. In one embodiment, the gene mutation targeted for repair is an inversion of intron 1. In one embodiment, the gene mutation targeted for repair is an inversion of intron 22.

The intron 22 inversion mutation of the F8 gene accounts for ˜45% of severe haemophilia A and is caused by an intra-chromosomal recombination within the gene. FIG. 1 shows a schematic illustration of the wild-type and intron 22-inverted FVIII loci (F8 & F8I22I). Transcription from the F8 promoter of both the F8 (wild-type) & F8I22I loci, which is normally functioning in both forms, yields polyadenylated mRNAs. The F8 mRNA has 26 exons, E1-E22 and E23-E26, all of which encode the amino acids found in the FVIII protein. Conversely, the F8I22I mRNA has at least 24 exons, E1-E22 (they are the same in F8 and thus encode FVIII amino acid sequence), and E23C & E24C (they are cryptic and encode no FVIII amino acid sequence). The sequence of intron-22, in both F8 & F8I22I, contains a bi-directional promoter that transcribes two additional mRNAs from the two genes: F8A, which is oriented oppositely to that of F8 & F8I22I and contains a single exon (box designated E1A), and F8B, which contains five exons that are oriented similarly transcriptionally to that of F8 & F8I22I and contains a single non-F8 first exon within I22 (box designated E1B) followed by four additional exons, which are identical to E23-E26 of F8. The F8A mRNA encodes the FVIIIA protein, which is now known as HAP40 (a cytoskeleton-interacting protein involved in endocytosis and thus functionally unrelated to the coagulation system) and has no FVIII amino acid sequence. The F8B mRNA encodes FVIII B, a protein with unknown function that has 8 non-FVIII amino acid residues at its N-terminus followed by 208 residues that represent FVIII residues 2125-2332.

3. Targeting Nucleases

The present invention provides for the targeting and repair of a mutated F8 gene in a subject with HA, including by introducing into a subject's cell one or more nucleic acids encoding a nuclease that specifically targets the F8 mutation. As discussed above, each subject's HA mutation for targeting and repair can be readily determined using techniques known in the art. The identified mutation in the subject can then be directly targeted by nucleases for correction. Alternatively, the subject's HA mutations can be corrected by targeting a region of the F8 gene upstream (or 5′) from where the mutation occurs, and adding back the corresponding downstream coding regions of the F8 gene. For example, intron 14 could be targeted by the nucleases. This allows for gene repair of downstream mutations (i.e. missense mutations in exon 15 to exon 26) and inversions (such as the intron 22 inversion), due to the replacement of exons 15 to 26 with the wild-type sequences. In other embodiments, the F8 gene can be targeted at additional regions upstream, in order to capture an increasing proportion of F8 gene mutations causing HA. Thus, the nucleases can be engineered to specifically target a subject's F8 mutation, or alternatively, may target regions upstream of a subject's F8 mutation, in order to correct the mutation.

In the methods and compositions set forth herein, the one or more nucleic acids encoding a nuclease that targets a mutation in F8 for repair, for example, an intron 22 mutation in human F8, can be, for example, a transcription activator—like effector nuclease (TALEN), a zinc finger nuclease (ZFN), or a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-associated (Cas) nuclease.

Transcription Activator-Like Effector Nucleases (TALENs)

Transcription Activator-Like Effector Nucleases (TALENs) are emerging as a preferred alternative to zinc finger nucleases (ZFNs) for certain types of genome editing. The C-terminus of the TALEN component carries nuclear localization signals (NLSs), allowing import of the protein to the nucleus. Downstream of the NLSs, an acidic activation domain (AD) is also present, which is probably involved in the recruitment of the host transcriptional machinery. The central region harbors the most fascinating feature of TALENs and the most versatile. It is made up of a series of nearly identical 34/35 amino acids modules repeated in tandem. Residues in positions 12 and 13 are highly variable and are referred to as repeat-variable di-residues (RVDs). Studies of TALENs such as AvrBs3 from X. axonopodis pv. vesicatoria and the genomic regions (e.g., promoters) they bind, led two teams to “crack the TALE code” by recognizing that each RVD in a repeat of a particular TALE determines the interaction with a single nucleotide. Most of the variation between TALEs relies on the number (ranging from 5.5 to 33.5) and/or the order of the quasi-identical repeats. Estimates using design criteria derived from the features of naturally occurring TALEs suggest that, on average, a suitable TALEN target site may be found every 35 base pairs in genomic DNA. Compared with ZFNs, the cloning process of TALENs is easier, the specificity of recognized target sequences is higher, and off-target effects are lower. In one study, TALENs designed to target CCR5 were shown to have very little activity at the highly homologous CCR2 locus, as compared with CCR5-specific ZFNs that had similar activity at the two sites.

FIGS. 2 and 3 are exemplary illustrations outlining the use of a nucleic acid encoding a TALEN nuclease that can be used to repair the F8 gene in, for example, a human with an intron-22 (I22)-inverted F8 locus, F8I22I. As illustrated in FIG. 2(A), the major transcription unit of the F8I22I locus consists of 24 exons, which are designated exons I-22 and exons 23C & 24C. The first 22 are the same as exons 1-22 of the wild-type FVIII structural locus (F8) but the last two (exon-23C & exon-24C) are cryptic and non-functional in non-hemophilic individuals as well as in patients whose HA is caused by F8 gene abnormalities other than the I22I-mutation. As illustrated in FIG. 2(B) the strategy to repair the I22I-mutation consists of introducing in the cell of the subject a nucleic acid encoding a functional TALEN—which is a heterodimeric nuclease comprised of a monomer subunit that binds 5′ of the desired genome editing site (TALEN-L) and one that binds 3′ of it (TALEN-R)—that is specific for a DNA sequence that is present in only a single copy per haploid human genome, which is approximately 1 kb downstream of the 3′-end of exon-22. Upon expression, once both monomers are bound to this specific sequence, their individual Fok1 nuclease domains dimerize to form the active enzyme that catalyzes a double-stranded (ds) break in the DNA between their binding sites. If a ds-DNA break occurs in the presence of a second nucleic acid, for example a nucleic acid comprising a native FVIII 3′ splice acceptor site operably linked to a nucleic acid encoding a truncated FVIII polypeptide encoding exons 23-26 (i.e., a “donor plasmid (DP)”), which contains a stretch of DNA with a left homology (HL) arm and right homology (HL) arm that have identical DNA sequences to that in the native chromosomal DNA 5′ and 3′ of the region flanking the break-point, homologous recombination (HR) occurs very efficiently. Following HR, the DNA segment between the left and right homology arms (which in this case contains a partial human F8 cDNA that contains, in-frame, all of exons 23-25 and the coding sequence of exon-26, with a functional 3′-splice site at its 5′-end) becomes permanently ligated/inserted into the chromosome. Since the DNA segment between the left and right homology arms comprises a partial human F8 cDNA (which, as shown in FIG. 2, contains, in-frame, all of exons 23-25 and the coding sequence of exon-26) fused at its 5′-end to a functional 3′-splice site, this TALEN catalyzes repair and converts F8I22I into wild-type F8-like locus and restore its ability to drive synthesis of a full-length fully functional wild-type FVIII protein.

FIG. 3 shows a functional heterodimeric TALEN, comprised of left and right monomer subunits (TALEN-L and TALEN-R), bound to its target “editing” sequence in intron 22 (I22) of the human FVIII structural locus (F8), ˜1 kb downstream of the 3′-end of exon-22 (FIG. 3). Because the target binding sequence of each monomer is the same in both a wild-type FVIII gene (F8) and an I22-inverted FVIII gene (F8I22I), this TALEN edits each locus equally well. Following binding of this TALEN's monomeric subunits to their target I22-sequences in the F8I22I locus of a patient with severe HA caused by the I22-inversion (I22I)-mutation, the individual Fok1 nuclease domains are able to form a homo-dimer, i.e. the active form of the enzyme, which catalyzes a double-stranded (ds) break in the DNA between the monomer binding sites. If a ds-DNA break occurs in the presence of a donor plasmid containing the replacement or “repairing” sequence, which contains a stretch of DNA with left and right arms that have identical DNA sequences to that in the native chromosomal DNA, in the region flanking the break-point (see FIG. 2), homologous recombination (HR) occurs very efficiently. Following HR, the DNA segment between the left and right homology arms (which, as shown in FIG. 2, contains a partial human F8 cDNA that contains, in-frame, all of exons 23-25 and the coding sequence of exon-26, with a functional 3′-splice site at its 5′-end—i.e., the repairing sequence) becomes permanently ligated/inserted into the chromosome. Because the DNA segment between the left and right homology arms comprises a partial human F8 cDNA (which, as shown in FIG. 2, contains, in-frame, all of exons 23-25 and the coding sequence of exon-26) fused at its 5′-end to a functional 3′-splice site, this TALEN catalyzes repair and converts F8I22I into wild-type F8-like locus and restore its ability to drive synthesis of a full-length fully functional wild-type FVIII protein.

Likewise, FIG. 4 shows a functional heterodimeric TALEN targeting a F8 mutation in canine, comprised of its left and right monomer subunits (TALEN-L and TALEN-R), bound to its target “editing” sequence in the intron-22 (I22) of the canine FVIII structural locus (cF8), ˜0.25 kb downstream of the 3′-end of exon-22. Because the target binding sequence of each monomer is the same in both a wild-type canine FVIII gene (cF8) and an I22-inverted FVIII gene (cF8I22I), this TALEN edits each locus equally well. Following binding of this TALEN's monomeric subunits to their target I22-sequences in the cF8I22I locus of a dog with severe HA caused by the I22-inversion (I22I)-mutation, their individual Fok1 nuclease domains are able to form a homo-dimer, i.e. the active form of the enzyme, which catalyzes a double-stranded (ds) break in the DNA between the monomer binding sites. If a ds-DNA break occurs in the presence of a donor plasmid, which contains a stretch of DNA with left and right arms that have identical DNA sequences to that in the native chromosomal DNA, in the region flanking the break-point (see FIG. 3 for the human F8 locus), homologous recombination (HR) occurs very efficiently. Following HR, the DNA segment between the left and right homology arms (which contains a partial cF8 cDNA that contains, in-frame, all of exons 23-25 and the coding sequence of exon-26, with a functional 3′-splice site at its 5′-end) becomes permanently ligated/inserted into the canine X-chromosome. Because the DNA segment between the left and right homology arms comprises a partial cF8 cDNA (which, as shown in FIG. 2 for the human F8I22I, contains, in-frame, all of canine exons 23-25 and the coding sequence of canine exon-26) fused at its 5′-end to a functional 3′-splice site, this TALEN catalyzes repair and converts cF8I22I into a wild-type cF8-like locus that restores its ability to drive synthesis of a full-length fully functional wild-type canine FVIII protein.

FIG. 5 illustrates a TALEN-mediated strategies to repair the human Factor VIII (FVIII) gene (F8) mutations in >50% of all patients with severe hemophilia-A (HA), including the highly recurrent intron-22 (I22)-inversion (I22I)-mutation. FIG. 5 highlights the TALEN approach linking Exon 22 of the F8 gene to a nucleic acid encoding a truncated FVIII polypeptide encoding exons 23-26. Panel A of FIG. 5 shows the specific F8 genomic DNA sequence (spanning genic base positions 126,625-126,693) within which a double-stranded DNA break is introduced (designated “Endonuclease domain” in Panel B) by this strategy's functional TALEN dimer. The left and right TALEN protein sequences for the variable DNA-binding domain are listed as Seq. ID. No. 4 and Seq. ID. No. 6, respectively. An example of DNA sequences encoding the left and right TALEN DNA-binding domains are listed as Seq. ID. No 5 and Seq. ID. No. 7, respectively. Because of the degeneracy of the genetic code, there are many possible constructs that can be used to encode TALEN DNA-binding domains. In some embodiments, the codons are optimized for expression of the DNA constructs. Panel A in FIG. 5 also shows the F8 genomic DNA sequence containing (i) the recognition sites for the left (TALEN_(L)-hF8_(E22/I22)) and right (TALEN_(R)-hF8_(E22/I22)) TALEN monomers comprising F8-TALEN-5 and (ii) the intervening spacer region within which the F8-TALEN-5′s endonuclease activity creates the double-stranded DNA breaks (DSDBs) required for inducing the physiologic cellular machinery that mediates the homology-dependent DNA repair pathway. Panel A in FIG. 5 also shows important orienting landmarks, including the following: (i) Nucleotide coordinates of this region (based on the February, 2009, human genome assembly [UCSC Genome Browser: http://genome.ucsc.edu/]) are numbered with respect to the wild-type F8 transcription unit, where the initial (5′-most) base of the F8 pre-mRNA (5′-base of exon-1 [E1]) is designated +1 or 1 (note that this base corresponds to X-chromosome position 154,250,998) and includes the appropriate intronic sequence bases in calculating the genomic base positioning; (ii) Relative location of the X-chromosome's centromere (X-Cen) and its long-arm telomere (Xq-Tel), as transcription of the wild-type F8 locus and all of its mutant alleles causing HA—with the exception of its two recurrent intronic inversions, the intron-1 (I1)-inversion (I1I)- and the I22I-mutations—is oriented towards X-Cen. Transcription of the I1- and I22-inverted F8 loci, in contrast, are oriented towards Xq-Tel. This strategy repairs (i) the highly recurrent I22I-mutation—also designated F8_(I22I)—which causes ˜45% of all unrelated patients with severe hemophilia-A (HA) and (ii) mutant F8 loci in ˜20% of all other patients with severe HA, who are either known or found to have any one of the >200 distinct mutations that have been found (according to the HAMSTeRS database of HA-causing F8 mutations) thus far to reside down-stream (i.e., 3′) of exon-22 (E22). The last codon of exon 22 encodes methionine (Met [M]) as translated residue 2,143 (2,124 in the mature FVIII protein secreted into plasma). Most mutations repaired are “previously known” (literature and/or HAMSTeRS or other databases), some have never been identified previously; the F8 abnormalities in this latter category are “private” (found only in this particular) to the patient/family.

Panel B in FIG. 5 shows the functional aspects of the TALENs including the overall DNA-binding domain (DBD) and the DBD-subunit repeats of the left and right monomers (TALEN_(L)-hF8_(E22/I22) and TALEN_(R)-hF8_(E22/I22)). Also shown are the (i) specific DNA sequences recognized by each TALEN monomer (shown in bold font immediately below each DBD-subunit); (ii) the spacer region between the DNA recognition sequences of the TALEN monomers contains the sequence within which the dimerized Fok1 catalytic domains, which form a functional endonuclease, introduce a double-stranded DNA break (DSDB). As shown in the lower left portion of FIG. 5, the introduction of a DSDB in the presence of homologous repair vehicle no. 5 (HRV5), the nucleotide sequence of which is provided below as Seq. ID. No. 12, results in the in-frame integration, immediately 3′ to exon 22, of the partial human F8 cDNA comprising exons 23, 24 and 25 and the protein coding sequence, or CDS, of exon 26 (designated hF8[E23-E25/E26_(CDS)]). In one embodiment, the TALEN constructs depicted in FIG. 5 can be used to repair all I22I inversion mutations (See #1 pathway). In another embodiment, the same constructs can be used to repair non-I22I F8 mutations that occur 3′ (i.e. downstream) of the exon-22/intron-22 junction (See #2 pathway).

FIG. 6 illustrates a TALEN-mediated strategy to repair the human Factor VIII (FVIII) gene (F8) mutations in >50% of all patients with severe hemophilia-A (HA), including the highly recurrent intron-22 (I22)-inversion (I22I)-mutation. FIG. 6 highlights the TALEN approach linking intron 22 of the F8 gene to a nucleic acid encoding a truncated FVIII polypeptide encoding exons 23-26. Panel A shows the specific F8 genomic DNA sequence within which a double-stranded DNA break is introduced (designated “Endonuclease domain” in Panel B) by this strategy's functional TALEN dimer. The left and right TALEN protein sequences for the variable DNA-binding domain are listed as Seq. ID. No. 8 and Seq. ID. No. 10, respectively. Examples of DNA sequences encoding the left and right TALEN DNA-binding domains are listed as Seq. ID. No. 9 and Seq. ID. No. 11, respectively. Because of the degeneracy of the genetic code, there are many possible constructs that can be used to encode TALEN DNA-binding domains. In some embodiments, the codons are optimized for expression of the DNA constructs. Panel A in FIG. 6 also shows important orienting landmarks, including the: (i) nucleotide coordinates of this region (based on the February, 2009, human genome assembly available at the UCSC Genome Browser: http://genome.ucsc.edu/) are numbered with respect to the wild-type F8 transcription unit, where the initial (5′-most) base of the F8 pre-mRNA (5′ most base of exon-1 [E1]) is designated +1 or 1 (note that this base corresponds to X-chromosome position 154,250,998) and includes the appropriate intronic sequence bases in calculating the genomic base positioning; (ii) relative location of the X-chromosome's centromere (X-Cen) and its long-arm telomere (Xq-Tel), as transcription of the wild-type F8 locus and all of its mutant alleles causing HA with the exception of its two recurrent intronic inversions, the intron-1 (I1)-inversion (I1I)- and the I22I-mutations is oriented towards X-Cen; Transcription of the I1- and I22-inverted F8 loci, in contrast, is oriented towards Xq-Tel. This strategy repairs (i) the highly recurrent I22I-mutation—also designated F8_(I22I)—which causes ˜45% of all unrelated patients with severe hemophilia-A (HA) and (ii) mutant F8 loci in ˜20% of all other patients with severe HA, who are either known or found to have any one of the >200 distinct mutations that have been found (according to the HAMSTeRS database of HA-causing F8 mutations) thus far to reside down-stream (i.e., 3′) of exon-22 (E22). The last codon of E22 entirely encodes methionine (Met [M]) as translated residue 2,143 (2,124 in the mature FVIII protein secreted into plasma). Most mutations repaired are “previously known” (literature and/or HAMSTeRS or other databases), but some have never been identified previously. The F8 abnormalities in this latter category are “private” (found only in this particular) to the patient/family.

Panel B in FIG. 6 shows the functional aspects of the TALENs including the overall DNA-binding domain (DBD) and the DBD-subunit repeats of the left and right monomers (TALEN_(L)-hF8_(I22) and TALEN_(R)-hF8_(I22)). Also shown are the (i) specific DNA sequences recognized by each TALEN monomer (shown in bold font immediately below each DBD-subunit); (ii) the spacer region between the DNA recognition sequences of the TALEN monomers contains the sequence within which the dimerized Fok1 catalytic domains, which form a functional endonuclease, introduce a double-stranded DNA break (DSDB). As shown in the lower left portion of FIG. 6, the introduction of a DSDB in the presence of a homologous repair vehicle, the nucleotide sequence of which is listed as Seq. ID. No. 13, results in the integration into intron 22 of a native F8 3′ splice acceptor site operably linked to a nucleic acid encoding F8 exons 23, 24 and 25 and the protein coding sequence, or CDS, of exon 26 (designated hF8[E23-E25/E26_(CDS)]). In one embodiment, the TALEN constructs depicted in FIG. 6 can be used to repair all I22I inversion mutations (See #1 pathway). In another embodiment, the same constructs are used to repair non-I22I F8 mutations that occur 3′ (i.e. downstream) of the exon-22/intron-22 junction (See #2 pathway).

In some embodiments, nucleic acids encoding nucleases specifically target intron1, intron14, or intron22. In some embodiments, nucleic acids encoding nucleases specifically target the exon1/intron1 junction; exon14/intron14 junction; or the exon22/intron22 junction.

FIG. 9 illustrates an example of a donor plasmid that can be used to repair the F8 gene at the exon22/intron22 junction using a TALEN nuclease, zinc finger nuclease, or cas nuclease approach. The donor plasmid contains the cDNA sequence for exons 23-26 of the F8 gene and a polyadenylation signal sequence flanked by two regions of homology to the F8 gene. The left homology region contains a DNA sequence (approximately 700 base pairs) that is homologous to part of Intron 21 and Exon22 of the F8 gene. The right homology region contains a DNA sequence (approximately 700 base pairs) that is homologous to part of intron 22 of the F8 gene. Upon successful homologous recombination into the F8 locus, the integrated construct expresses the resulting mRNA encoding the wild-type (corrected) version of the F8 protein. The sequence of the plasmid depicted in FIG. 9 is listed as Seq. ID. No. 12. The annotation of Seq. ID. No. 12 is provided in Table 1 below.

TABLE 1 Repair vehicle targeted to the Exon 22-Intron 22 junction of F8 LOCUS RepairVehicle 7753 bp DNA linear FEATURES Location/Qualifiers misc_feature 21..327 /note=“f1 origin (-) ” misc_feature 6765..7625 /note=“<= Ampicillin” misc_feature 471..614 /label=<= lacZ A misc_feature 626..644 /note=“T7 promoter =>” misc_feature 5564..5583 /note=“T3 promoter =>” misc_feature 6765..7625 /note=“<= Orf1” misc_feature 7667..7695 /note=“<= AmpR promoter” misc_feature 658..740 /note=“MCS” misc_feature 1446..2072 /note=“Exons 23-26 (cDNA seq) ” misc_feature 1730..1737 /note=“Create NotI site” misc_feature 2082..2707 /note=“hGH polyA” misc_feature 1785..1787 /note=“ns-SNP: A6940G (M2238V) ” misc_feature 3408..4160 /note=“HSV-TK promoter ” misc_feature 4161..5546 /note=“HSV-TK gene and TK pA Terminator ” misc_feature 741..745 /note=“Create site for cloning” misc_feature 5547..5551 /note=“Create site for cloning” misc_feature 746..1445 /note=“Left homolgy arm (700 bp) ” misc_feature 1290..1445 /note=“Exon 22” misc_feature 1433..1445 /note=“Partial Left TALEN recognition site” misc_feature 2708..3407 /note=“Right homology arm (700 bp) ” misc_feature 2708..2716 /note=“Partial Right TALEN recognition site” misc_feature 2708..3407 /note=“Partial Intron 22” misc_feature 746..1289 /note=“Partial Intron 21” source 1..7753 /dnas_title=“RepairVehicle E22-I22 pBluescript”

FIG. 10 illustrates an example of a donor plasmid that may be used to repair the F8 gene using a TALEN nuclease, zinc finger nuclease, or cas nuclease approach. The donor plasmid contains the cDNA sequence for exons 2-26 of the F8 gene flanked by two regions of homology to the F8 gene. The left homology region contains a DNA sequence that is homologous to part of the F8 promoter and part of Exon 1. The right homology region contains a DNA sequence that is homologous to part of intron 1. Upon successful homologous recombination into the F8 gene, the integrated construct expresses the resulting mRNA encoding the wild-type (corrected) version of the F8 protein. The donor sequence is cloned into plasmid (p)BlueScript-II KS-minus (pBS-II-KS[-]). The donor plasmid is used with a TALEN, ZFN, or CRISPR/Cas genomic editing strategy. The sequence of the plasmid depicted in FIG. 10 is listed as Seq. ID. No. 13. The annotation of Seq. ID. No. 13 is provided in Table 2 below.

TABLE 2 Repair vehicle targeted to the Exon 1-Intron 1 junction of F8 LOCUS RepairVehicle 11418 bp DNA linear FEATURES Location/Qualifiers misc_feature 21..327 /note=“f1 origin (-) ” misc_feature 10430..11290 /note=“<= Ampicillin” misc_feature 471..614 /label=<= lacZ A misc_feature 626..644 /note=“T7 promoter =>” misc_feature 9229..9248 /note=“<= T3 promoter” misc_feature 10430..11290 /note=“<= Orf1” misc_feature 11332..11360 /note=“<= AmpR promoter” misc_feature 658..740 /note=“MCS” misc_feature 5780..6405 /note=“hGH polyA” misc_feature 7073..7825 /note=“HSV-TK promoter ” misc_feature 7826..9211 /note=“HSV-TK gene and TK pA Terminator ” misc_feature 740..745 /note=“Create site for cloning” misc_feature 1540..5770 /note=“Exons 2-26 BDD (cDNA seq) ” misc_feature 2664..2669 /note=“Create ClaI site” misc_feature 2903..2905 /note=“ns-SNP: G1679A (R484H) ” misc_feature 3680..3685 /note=“BDD (Ser743 - Gln1638) ” misc_feature 5428..5435 /note=“Create NotI site” misc_feature 5768..5768 /dnas_title=“Stop” /vntifkey=“21” /label=Stop misc_feature 5483..5485 /note=“ns-SNP: A6940G (M2238V) ” insertion_seq 3934..5770 /dnas_title=“Tg” /vntifkey=“14” /label=Tg misc_feature 9212..9217 /note=“Create site for cloning” misc_feature 9212..9212 /note=“MCS” misc_feature 746..1539 /note=“Left homolgy arm (794bp) ” misc_feature 746..1237 /note=“Partial F8 promoter” misc_feature 1238..1539 /note=“Partial Exon 1” misc_feature 6406..7072 /note=“Right homology arm (667 bp) ” misc_feature 6406..7072 /note=“Partial intron 1” source 1..11418 /dnas_title=“RepairVehicle E1-I1 pBluescript”

FIG. 11 illustrates an example of a donor plasmid that is used to repair the F8 gene in intron 22 using a TALEN nuclease, zinc finger nuclease, or cas nuclease approach. The donor plasmid contains a 3′ splice site, the cDNA sequence for exons 23-26 of the F8 gene, and a polyadenylation signal sequence flanked by two regions of homology to the F8 gene. The left homology region contains a DNA sequence (approximately 700 base pairs) that is homologous to part of Intron 22 of the F8 gene. The right homology region contains a DNA sequence (approximately 700 base pairs) that is homologous to part of intron 22 of the F8 gene. Upon successful homologous recombination into the F8 locus, the integrated construct expresses the resulting mRNA encoding the wild-type (corrected) version of the F8 protein. The sequence of the plasmid depicted in FIG. 11 is listed as Seq. ID. No. 14. The annotation of Seq. ID. No. 14 is provided in Table 3 below.

TABLE 3 Repair vehicle targeted to Intron 22 of F8 LOCUS RepairVehicle 7755 bp DNA linear FEATURES Location/Qualifiers misc_feature 21..327 /note=“f1 origin (-) ” misc_feature 6767..7627 /note=“<=Ampicillin” misc_feature 471..614 /label=<= lacZ A misc_feature 626..644 /note=“T7 promoter =>” misc_feature 5566..5585 /note=“T3 promoter =>” misc_feature 6767..7627 /note=“<= Orf1” misc_feature 7669..7697 /note=“<= AmpR promoter” misc_feature 658..740 /note=“MCS” misc_feature 1448..2074 /note=“Exons 23-26 (cDNA seq) ” misc_feature 1732..1739 /note=“Create NotI site” misc_feature 2084..2709 /note=“hGH polyA” misc_feature 1787..1789 /note=“ns-SNP: A6940G (M2238V) ” misc_feature 3410..4162 /note=“HSV-TK promoter ” misc_feature 4163..5548 /note=“HSV-TK gene and TK pA Terminator ” misc_feature 741..745 /note=“Create site for cloning” misc_feature 5549..5553 /note=“Create site for cloning” misc_feature 746..1445 /note=“Left homology arm (700 bp) ” misc_feature 1437..1445 /note=“Partial Left TALEN recognition site” misc_feature 2710..3409 /note=“Right homolgy arm (700 bp) ” misc_feature 2710..2719 /note=“Partial Right TALEN recognition site” misc_feature 746..1445 /note=“Partial Intron 22” misc_feature 2710..3409 /note=“Partial Intron 22” misc_feature 1446..1447 /note=“3′ spice site” source 1..7755 /dnas_title=“RepairVehicle 122 pBluescript”

FIG. 12 illustrates an example of a donor plasmid that is used to repair the F8 gene in intronl using a TALEN nuclease, zinc finger nuclease, or cas nuclease approach. The donor plasmid contains a 3′ splice site, the cDNA sequence of the F8 gene for exons 2-26 lacking the B-domain (B-domain deleted (BDD) version of the F8 gene), and a polyadenylation signal sequence flanked by two regions of homology to the F8 gene. The left homology region contains a DNA sequence (approximately 700 base pairs) that is homologous to part of Exon 1 and Intron 1 of the F8 gene. The right homology region contains a DNA sequence (approximately 700 base pairs) that is homologous to part of intron 1 of the F8 gene. Upon successful homologous recombination into the F8 locus, the integrated construct expresses the resulting mRNA encoding the wild-type (corrected) version of the F8 protein. The sequence of the plasmid depicted in FIG. 12 is listed as Seq. ID. No. 15. The annotation of Seq. ID. No. 15 is provided in Table 4 below.

TABLE 4 Repair vehicle targeted to Intron 1 of F8 LOCUS RepairVehicle 11359 bp DNA linear FEATURES Location/Qualifiers misc_feature 21..327 /note=“f1 origin (-) ” misc_feature 10371..11231 /note=“<= Ampicillin” misc_feature 471..614 /label=<= lacZ A misc_feature 626..644 /note=“T7 promoter =>” misc_feature 9170..9189 /note=“<= T3 promoter” misc_feature 10371..11231 /note=“<= Orf1” misc_feature 11273..11301 /note=“<= AmpR promoter” misc_feature 658..740 /note=“MCS” misc_feature 874..1187 /note=“Exon 1” misc_feature 1436..1445 /note=“Partial Left TALEN recognition site” misc_feature 5688..6313 /note=“hGH polyA” misc_feature 6314..7013 /note=“Right homology arm (700 bp) ” misc_feature 6314..6322 /note=“Partial Right TALEN recognition site” misc_feature 7014..7766 /note=“HSV-TK promoter ” misc_feature 7767..9152 /note=“HSV-TK gene and TK pA Terminator ” misc_feature 746..1445 /note=“Left homolgy arm (700 bp) ” misc_feature 746..873 /note=“Partial F8 promoter” misc_feature 740..745 /note=“Create site for cloning” misc_feature 6314..7013 /note=“Partial Intron 1” misc_feature 1448..5678 /note=“Exons 2-26 BDD (cDNA seq) ” misc_feature 1446..1447 /note=“3′ spice site” misc_feature 2572..2577 /note=“Create ClaI site” misc_feature 2811..2813 /note=“ns-SNP: G1679A (R484H) ” misc_feature 3588..3593 /note=“BDD (Ser743 - Gln1638) ” misc_feature 5336..5343 /note=“Create NotI site” misc_feature 5676..5676 /dnas_title=“Stop” /vntifkey=“21” /label=Stop misc_feature 5391..5393 /note=“ns-SNP: A6940G (M2238V) ” insertion_seq 3842..5678 /dnas_title=“Tg” /vntifkey=“14” /label=Tg misc_feature 9153..9158 /note=“Create site for cloning” misc_feature 9153..9153 /note=“MCS” source 1..11359 /dnas_title=“RepairVehicle I1 pBluescript”

In one embodiment, the integration matrix component for each of these distinct homologous donor plasmid is either a cDNA that is linked to the immediately upstream exon or a cDNA that has a functional 3′-intron-splice-junction so that the cDNA sequence is linked through the RNA intermediate following removal of the intron. In one embodiment, the donor plasmid is personalized, on an individual basis, so that each patient's gene that is repaired expresses the form of the FVIII protein that they are maximally tolerant of.

Zinc Finger Nucleases (ZFNs)

Engineered nucleases have emerged as powerful tools for site specific editing of the genome. For example, zinc finger nucleases (ZFNs) are hybrid proteins containing the zinc-finger DNA-binding domain present in transcription factors and the non-specific cleavage domain of the endonuclease Fok1. (Li et al., In vivo genome editing restores haemostasis in a mouse model of haemophilia, Nature 2011 Jun. 26; 475(7355):217-21).

The same sequences targeted by the TALEN approach, discussed above, can also be targeted by the zinc finger nuclease approach for genome editing. Zinc finger nucleases (ZFNs) are a class of engineered DNA-binding proteins that facilitate targeted editing of the genome by creating double-strand breaks in DNA at user-specified locations. Each Zinc Finger Nuclease (ZFN) consists of two functional domains: 1) a DNA-binding domain comprised of a chain of two-finger modules, each recognizing a unique hexamer (6 bp) sequence of DNA, wherein two-finger modules are stitched together to form a Zinc Finger Protein, each with specificity of ≧24 bp, and 2) a DNA-cleaving domain comprised of the nuclease domain of Fok I. The DNA-binding and DNA-cleaving domains are fused together and recognize the targeted genomic sequences, allowing the Fok1 domains to form a heterodimeric enzyme that cleaves the DNA by creating double stranded breaks.

Zinc finger nucleases can be readily made by using techniques known in the art (Wright D A, et al. Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly. Nat Protoc. 2006; 1(3):1637-52). Engineered zinc finger nucleases can stimulate gene targeting at specific genomic loci in animal and human cells. The construction of artificial zinc finger arrays using modular assembly has been described. The archive of plasmids encoding more than 140 well-characterized zinc finger modules together with complementary web-based software for identifying potential zinc finger target sites in a gene of interest has also been described. These reagents enable easy mixing-and-matching of modules and transfer of assembled arrays to expression vectors without the need for specialized knowledge of zinc finger sequences or complicated oligonucleotide design (Wright D A, et al. Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly. Nat Protoc. 2006; 1(3):1637-52). Any gene in any organism can be targeted with a properly designed pair of ZFNs. Zinc-finger recognition depends only on a match to the target DNA sequence (Carroll, D. Genome engineering with zinc-finger nucleases. Genetics Society of America, 2011, 188(4), pp 773-782).

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR Associated (Cas) Nucleases

In addition to the current protein-based targeting methods (TALEN and Zinc Finger) useful for gene targeting, there is another system for genome editing that uses a short RNA to guide a nuclease to the DNA target. This system is called the CRISPR technology. (Mali P, Yang L, Esvelt K M, Aach J, Guell M, DiCarlo J E, Norville J E, Church G M. RNA-guided human genome engineering via Cas9. Science. 2013 Feb. 15; 339(6121):823-6; Gasiunas G, Barrangou R, Horvath P, Siksnys V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci USA. 2012 Sep. 25; 109(39):E2579-86. Epub 2012 Sep. 4).

The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR Associated (Cas) system was discovered in bacteria and functions as a defense against foreign DNA, either viral or plasmid. In bacteria, the endogenous CRISPR/Cas system targets foreign DNA with a short, complementary single-stranded RNA (CRISPR RNA or crRNA) that localizes the Cas9 nuclease to the target DNA sequence. The DNA target sequence can be on a plasmid or integrated into the bacterial genome. The crRNA can bind on either strand of DNA and the Cas9 cleaves both strands (double strand break, DSB). A recent in vitro reconstitution of the Streptococcus pyogenes type II CRISPR system demonstrated that crRNA fused to a normally trans-encoded tracrRNA is sufficient to direct Cas9 protein to sequence-specifically cleave target DNA sequences matching the crRNA. The fully defined nature of this two-component system allows it to function in the cells of eukaryotic organisms such as yeast, plants, and even mammals. By cleaving genomic sequences targeted by RNA sequences, such a system greatly enhances the ease of genome engineering.

The crRNA targeting sequences are transcribed from DNA sequences known as protospacers. Protospacers are clustered in the bacterial genome in a group called a CRISPR array. The protospacers are short sequences (˜20 bp) of known foreign DNA separated by a short palindromic repeat and kept like a record against future encounters. To create the CRISPR targeting RNA (crRNA), the array is transcribed and the RNA is processed to separate the individual recognition sequences between the repeats. In the Type II system, the processing of the CRISPR array transcript (pre-crRNA) into individual crRNAs is dependent on the presence of a trans-activating crRNA (tracrRNA) that has sequence complementary to the palindromic repeat. When the tracrRNA hybridizes to the short palindromic repeat, it triggers processing by the bacterial double-stranded RNA-specific ribonuclease, RNase III. Any crRNA and the tracrRNA can then both bind to the Cas9 nuclease, which then becomes activated and specific to the DNA sequence complimentary to the crRNA. (Mali P, Yang L, Esvelt K M, Aach J, Guell M, DiCarlo J E, Norville J E, Church G M. RNA-guided human genome engineering via Cas9. Science. 2013 Feb. 15; 339(6121):823-6; Gasiunas G, Barrangou R, Horvath P, Siksnys V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci USA. 2012 Sep. 25; 109(39):E2579-86. Epub 2012 Sep. 4).

The double-strand DNA breakages (DSDB) induced by the TALEN approach overlaps with the 6 distinct sites of DSDB induced by Cas9, via targeting by 6 distinct CRISPR-guide RNAs [F8-CRISPR/Cas9-1 (F8-Ex1/Int1), F8-CRISPR/Cas9-2 (F8-Int1), F8-CRISPR/Cas9-3 (F8-Ex14/Int14), F8-CRISPR/Cas9-4 (F8-Int14), F8-CRISPR/Cas9-5 (F8-Ex22/Int22), F8-CRISPR/Cas9-6 (F8-Int22)]. This allows use of the same 6 distinct homologous donor sequences with all three genome editing approaches, including the TALEN nuclease, the zinc finger nuclease (ZFN), and the CRISPR-associated (Cas) nuclease.

FIG. 13 illustrates a CRISPR/Cas9-mediated strategy to repair the human Factor VIII (FVIII) gene (F8) mutations in ˜95% of all patients with severe hemophilia-A (HA), including the highly recurrent intron-1 (I1)-inversion (I1I)-mutation as well as the intron-22 (I22)-inversion (I22I)-mutation. FIG. 13 shows the specific F8 genomic DNA sequence (spanning genic base positions 172-354 at intron 1) within which a double-stranded (ds)-DNA break is introduced (designated “Endonuclease target” in this panel) by this strategy's wild-type (wt) CRISPR/Cas9 ds-DNase in which both of its endonuclease domains are catalytically functional (“hF8-CRISPR/Cas9wt-1”). This panel also shows important orienting landmarks, including the following: (i) Nucleotide coordinates of this region (based on the February, 2009, human genome assembly [UCSC Genome Browser: http://genome.ucsc.edu/]) are numbered with respect to the wild-type F8 transcription unit, where the initial (5′-most) base of the F8 pre-mRNA (5′-base of exon-1 [El]) is designated +1 or 1 (note that this base corresponds to X-chromosome position 154,250,998) and include the appropriate intronic sequence bases in calculating the genomic base positioning; (ii) Relative location of the X-chromosome's centromere (X-Cen) and its long-arm telomere (Xq-Tel), as transcription of the wild-type F8 locus and all of its mutant alleles causing HA with the exception of its two recurrent intronic inversions, the I1I- and the I22I-mutations is oriented towards X-Cen. Transcription of the I1- and I22-inverted F8 loci, in contrast, are oriented towards Xq-Tel. This strategy repairs (i) the highly recurrent I22I-mutation—also designated F8_(I22I)—which causes ˜45% of all unrelated patients with severe hemophilia-A (HA) and (ii) mutant F8 loci in ˜90-95% of all other patients with severe HA, who are either known or found to have any one of the >1,500 distinct mutations that have been found (according to the HAMSTeRS database of HA-causing F8 mutations) thus far to reside down-stream (i.e., 3′) of exon-1 (E1). The last codon of E1 partially encodes the translated residue 48 (29 in the mature FVIII protein secreted into plasma). Most mutations repaired are “previously known” (literature and/or HAMSTeRS or other databases). Some have never been identified previously. These F8 abnormalities in this latter category are “private” (found only in this particular) to the patient/family. Finally, FIG. 13 shows the functional aspects of hF8-CRISPR/Cas9wt-1 including the overall DNA-binding domain of the CRISPR-associated guide (g)RNA as well as the (i) Protospacer adjacent motif (PAM), which is the site at which the DNase function of Cas9 introduces the ds-DNA break (DSDB); and (ii) The Transactivating Crispr-RNA (TrCr-RNA), which is covalently attached the gRNA as is what brings the Cas9 endonuclease to the genomic DNA target for digestion. The introduction of a DSDB in the presence of a homologous repair vehicle, results in the in-frame integration, immediately 3′ to E1, of one of either two partial human F8 cDNAs comprising either (i) exons 2-25 and the protein coding sequence, or CDS, of exon 26 (designated hF8[E2-E25/E26_(CDS)]), which effects repair of the F8 gene such that it now encodes a full-length wild-type FVIII protein; or (ii) Exons 2-13 entirely linked next to the very 5′-most end of exon-14 (E14), which in turn is linked covalently to the very 3′-most end of E14 (i.e., a B-domain-deleted [BDD]-F8 cDNA), which is then covalently linked to Exons 15-25 entirely, and then the protein coding sequence, or CDS, of exon 26 (designated hF8[E2-E13/E14-BDD/E15-E25/E26_(CDS)]), which effects repair of the F8 gene such that it now encodes a BDD-engineered FVIII protein, which is fully functional in FVIII:C activity. The homologous repair vehicle is selected to have a F8 cDNA with the appropriate alleles at all ns-SNP sites so that the patient can receive a “matched” gene repair or at least a least mismatched repair.

The left homology arm of the homologous repair vehicle for Homologous Repair Vehicle No. 1 (HRV1) for hF8-CRISP/Cas9wt-1 is listed as Seq. ID. No. 17 and comprises the first 1114 bases of the human F8 genomic DNA (which is shown here as single-stranded and representing the sense strand) and contains 800 bp of the immediately 5′-promoter region of the human F8 gene and all 314 bp of the F8 exon-1 (E1), including its 171 bp 5′-UTR and its 143 bp of protein (en)coding sequence (CDS). The actual left homologous arm (LHA) of the homologous repair vehicle (HRV1), which is used for this CRISPR/Cas9-mediated F8 gene repair (that occurs at the E1/intron-1 [I1] junction of a given patient's endogenous mutant F8), contains at least 500 bp of this genomic DNA sequence (i.e., from it's very 3′-end, which corresponds to the second base of the codon for translated residue 48 of the wild-type FVIII protein and residue 29 of the mature FVIII protein found in the circulation) and could include it all, if, for example, we find that full-length F8 gene repair can be effected efficiently in the future. In this instance, the integration matrix would then follow the LHA of this HRV1, and be covalently attached to it, and this integration matrix contains (in-frame with each other and with the 3′-end of the patient's native exon-1, which is utilized in situ, along with his native F8 promoter, to regulate expression of the repaired F8 gene), all of F8 exons 2-25, and the protein CDS of exon-25, followed by the functional mRNA 3′-end forming signals of the human growth hormone gene (hGH-pA). The F8 cDNA from exons 2-25 and the CDS of exon-26 to be used in the homologous repair vehicle is listed as Seq. ID. No. 18 and follows the left homology arm, and in this example represents the haplotype (H)3 encoding wild-type variant of F8, which can be used to cure, for example, patients with the I1I-mutation and the I22I-mutation, that arose on an H3-background haplotype. This following protein encoding cDNA sequence contains 6,909 bp of the entire 7,053 bp of F8 protein encoding sequence (i.e., the first 144 bp of protein CDS from FVIII, from its initiator methionine, is not shown, as this is contained in exon-1, which is provided by the patient's own endogenous exon-1, providing it is not mutant and thus precluding the repair event). The right homology arm of the homologous repair vehicle for the cas nuclease approach is listed as Seq. ID. No. 19 and includes 1109 bases of human F8 genomic DNA (which is shown here as single-stranded and representing the sense strand) from the F8 gene intron 1.

4. Replacement Sequence

As described above, following the introduction of the targeting nuclease into the cell, the nuclease, upon dimerization, catalyzes a double stranded break in the DNA between their binding sites. If a double stranded break occurs in the presence of, for example, a donor plasmid (DP), which contains a stretch of DNA with a left homology (HL) and right homology (HR) arm that have identical DNA sequences to that in the native chromosomal DNA 5′ and 3′ of the region flanking the break-point, homologous recombination occurs very efficiently. Accordingly, the present invention includes the introduction of a nucleic acid sequence that serves as a donor sequence during homologous recombination which includes a partial F8 gene that replaces, and thus repairs, the mutated portion of the subject's F8 gene.

The donor sequence nucleic acid comprises (i) a nucleic acid encoding a truncated FVIII polypeptide or (ii) a native F8 3′ splice acceptor site operably linked to a nucleic acid encoding a truncated FVIII polypeptide that contains a non-mutated portion of the FVIII protein. The donor sequence is flanked on each side by regions of nucleic acid which are homologous to the F8 gene. Each of these homologous regions can include about 20, 50, 75, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000 or more nucleotides homologous with the subject's F8 gene. In embodiments, each of the homologous regions flanking the donor sequence is between about 200 to about 1,200 nucleotides, between 400 and about 1000 nucleotides, or between about 600 and about 900 nucleotides. In one embodiment, each homologous region is between about 800 and about 900 nucleotides. Thus, each donor sequence nucleic acid includes a donor sequence replacing an endogenous mutation in the subject's F8 gene, and 5′ and 3′ flanking sequences which are homologous to the F8 gene.

The donor sequence is derived based on the specific mutation within the subject's F8 gene targeted for replacement and repair. Accordingly, the length of the donor sequence can vary. For example, when repairing a point mutation, the donor sequence can include only a small number of replacement nucleotide sequences compared with, for example, a donor sequence derived for repairing an inversion such as an intron 22 inversion. Therefore, a donor sequence can be of any length, for example between 2 and 10,000 nucleotides in length (or any integer value there between or there above), preferably between about 100 and 1,000 nucleotides in length (or any integer there between), more preferably between about 200 and 500 nucleotides in length. The designing of donor sequence nucleic acids is known in the art, for example, see Cermak et al., Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting, Nucleic Acid Res. 2011 Sep. 1; 39 (17):7879.

In one embodiment of the present invention, the gene mutation targeted for repair is a point mutation, and the donor sequence includes a nucleic acid sequence that replaces the point mutation with a sequence that does not include the point mutation, for example, the wild-type F8 sequence. In one embodiment, the gene mutation targeted for repair is a deletion and the donor sequence includes a nucleic acid sequence that replaces the deletion with a sequence that does not include the deletion, for example, the wild-type F8 sequence.

In one embodiment, the gene mutation targeted for repair is an inversion, and the donor sequence includes a nucleic acid sequence that encodes a truncated FVIII polypeptide that, upon insertion into the F8 genome, repairs the inversion and provides for the production of a functional FVIII protein. In one embodiment, the gene mutation targeted for repair is an inversion of intron 1. In one embodiment, the gene mutation targeted for repair is an inversion of intron 22, and the donor sequence includes a nucleic acid that encodes all of exons 23-25 and the coding sequence of exon-26.

In any of the methods described herein, the donor sequence can contain sequences that are homologous, but not identical (for example, contain nucleic acid sequence encoding wild-type amino acids or differing ns-SNP amino acids), to genomic sequences in the region of interest, thereby stimulating homologous recombination to insert a non-identical sequence in the region of interest. Thus, in certain embodiments, portions of the donor sequence that are homologous to sequences in the region of interest exhibit between about 80 to about 99% sequence identity to the genomic sequence that is replaced. In other embodiments, the homology between the donor and genomic sequence is higher than 99%, for example if only 1 nucleotide differs as between donor and genomic sequences of over 100 contiguous base pairs. In certain cases, a non-homologous portion of the donor sequence can contain sequences not present in the region of interest, such that new sequences are introduced into the region of interest. In these instances, the non-homologous sequence is generally flanked by sequences of 50-1,000 base pairs, or any number of base pairs greater than 1,000, that are homologous or identical to sequences in the region of interest. In other embodiments, the donor sequence is non-homologous to the first sequence, and is inserted into the genome by non-homologous recombination mechanisms.

5. Targeted Cells

The gene targeting and repair approaches using the different nucleases described above can be carried out using many different target cells. For example, the transduced cells may include endothelial cells, hepatocytes, or stem cells. In one embodiment, the cells can be targeted in vivo. In one embodiment, the cells can be targeted using ex vivo approaches and reintroduced into the subject.

BOECs

In one embodiment, the target cells from the subject are endothelial cells. In one embodiment, the endothelial cells are blood outgrowth endothelial cells (BOECs). Characteristics that render BOECs attractive for gene repair and delivery include the: (i) ability to be expanded from progenitor cells isolated from blood, (ii) mature endothelial cell, stable, phenotype and normal senescence (˜65 divisions), (iii) prolific expansion from a single blood sample to 1019 BOECs, (iv) resilience, which unlike other endothelial cells, permits cryopreservation and hence multiple doses for a single patient prepared from a single isolation. Methods of isolation of BOECs are known, where the culture of peripheral blood provides a rich supply of autologous, highly proliferative endothelial cells, also referred to as blood outgrowth endothelial cells (BOECs). Bodempudi V, et al., Blood outgrowth endothelial cell-based systemic delivery of antiangiogenic gene therapy for solid tumors. Cancer Gene Ther. 2010 December; 17(12):855-63.

Studies in animal models have revealed properties of blood outgrowth endothelial cells that indicate that they are suitable for use in ex vivo gene repair strategies. For example, a key finding concerning the behavior of canine blood outgrowth endothelial cells (cBOECs) is that cBOECs persist and expand within the canine liver after infusion. Milbauer L C, et al. Blood outgrowth endothelial cell migration and trapping in vivo: a window into gene therapy. 2009 April; 153(4):179-89. Whole blood clotting time (WBCT) in the HA model was also improved after administration of engineered cBOECs. WBCT dropped from a pretreatment value of under 60 min to below 40 min and sometimes below 30 min. Milbauer L C, et al., Blood outgrowth endothelial cell migration and trapping in vivo: a window into gene therapy. 2009 April; 153(4):179-89.

LSECs

In one embodiment, the target cells from the subject are hepatocytes. In one embodiment, the cell is a liver sinusoidal endothelial cell (LSECs). Liver sinusoidal endothelial cells (LSEC) are specialized endothelial cells that play important roles in liver physiology and disease. Hepatocytes and liver sinusoidal endothelial cells (LSECs) are thought to contribute a substantial component of FVIII in circulation, with a variety of extra-hepatic endothelial cells supplementing the supply of FVIII.

In one embodiment, the present invention targets LSEC cells, as LSEC cells likely represent the main cell source of FVIII. Shahani, T, et al., Activation of human endothelial cells from specific vascular beds induces the release of a FVIII storage pool. Blood 2010; 115(23):4902-4909. In addition, LSECs are believed to play a role in induction of immune tolerance. Onoe, T, et al., Liver sinusoidal endothelial cells tolerize T cells across MHC barriers in mice. J Immunol 2005; 175(1):139-146. Methods of isolation of LSECs are known in the art. Karrar, A, et al., Human liver sinusoidal endothelial cells induce apoptosis in activated T cells: a role in tolerance induction. Gut. 2007 February; 56(2): 243-252.

iPSCs

In one embodiment, the transduced cells from the subject are stem cells. In one embodiment, the stem cells are induced pluripotent stem cells (iPSCs). Induced pluripotent stem cells (iPSCs) are a type of pluripotent stem cell artificially derived from a non-pluripotent cell, typically an adult somatic cell, by inducing expression of specific genes and factors important for maintaining the defining properties of embryonic stem cells. Induced pluripotent stem cells (iPSCs) have been shown in several examples to be capable of site specific gene targeting by nucleases. Ru, R. et al. Targeted genome engineering in human induced pluripotent stem cells by penetrating TALENs. Cell Regeneration. 2013, 2:5; Sun N, Zhao H. Seamless correction of the sickle cell disease mutation of the HBB gene in human induced pluripotent stem cells using TALENs. Biotechnol Bioeng. 2013. Aug 8. Induced pluripotent stem cells (iPSCs) can be isolated using methods known in the art. Lorenzo, I M. Generation of Mouse and Human Induced Pluripotent Stem Cells (iPSC) from Primary Somatic Cells. Stem Cell Rev. 2013 August; 9(4):435-50.

Co-Cultured Cells

As discussed above, a number of different cells types may be targeted for repair. However, pure populations of some cell types may not promote sufficient homing and implantation upon reintroduction to provide extended and sufficient expression of the corrected F8 gene. Therefore, some cell types may be co-cultured with different cell types to help promote cell properties (i.e. ability of cells to engraft in the liver).

In one embodiment, the transduced cells are from blood outgrowth endothelial cells (BOECs) that have been co-cultured with additional cell types. In one embodiment, the transduced cells are from blood outgrowth endothelial cells (BOECs) that have been co-cultured with hepatocytes or liver sinusoidal endothelial cell (LESCs) or both. In one embodiment, the transduced cells are from blood outgrowth endothelial cells (BOECs) that have been co-cultured with induced pluripotent stem cells (iPSCs).

6. Cell Delivery

Methods of nucleic acid delivery are well known in the art. (See, e.g., WO 2012051343). In the methods provided herein, the described nuclease encoding nucleic acids can be introduced into the cell as DNA or RNA, single-stranded or double-stranded and can be introduced into a cell in linear or circular form. In one embodiment, the nucleic acids encoding the nuclease are introduced into the cell as mRNA. The donor sequence can introduced into the cell as DNA single-stranded or double-stranded and can be introduced into a cell in linear or circular form. If introduced in linear form, the ends of the nucleic acids can be protected (e.g., from exonucleolytic degradation) by methods known to those of skill in the art. For example, one or more dideoxynucleotide residues are added to the 3′ terminus of a linear molecule and/or self-complementary oligonucleotides are ligated to one or both ends. See, for example, Chang et al. (1987) Proc. Natl. Acad. Sci. USA 84:4959-4963; Nehls et al. (1996) Science 272:886-889. Additional methods for protecting exogenous polynucleotides from degradation include, but are not limited to, addition of terminal amino group(s) and the use of modified internucleotide linkages such as, for example, phosphorothioates, phosphoramidates, and O-methyl ribose or deoxyribose residues.

The nucleic acids can be introduced into a cell as part of a vector molecule having additional sequences such as, for example, replication origins, promoters and genes encoding antibiotic resistance. Moreover, the nucleic acids can be introduced as naked nucleic acid, as nucleic acid complexed with an agent such as a liposome or poloxamer, or can be delivered by viruses (e.g., adenovirus, AAV, herpesvirus, retrovirus, lentivirus).

The nucleic acids may be delivered in vivo or ex vivo by any suitable means. Methods of delivering nucleic acids are described, for example, in U.S. Pat. Nos. 6,453,242; 6,503,717; 6,534,261; 6,599,692; 6,607,882; 6,689,558; 6,824,978; 6,933,113; 6,979,539; 7,013,219; and 7,163,824.

Any vector systems may be used including, but not limited to, plasmid vectors, retroviral vectors, lentiviral vectors, adenovirus vectors, poxvirus vectors; herpesvirus vectors and adeno-associated virus vectors, etc. See, also, U.S. Pat. Nos. 6,534,261; 6,607,882; 6,824,978; 6,933,113; 6,979,539; 7,013,219; and 7,163,824. Furthermore, any of these vectors may comprise one or more of the sequences needed for treatment. Thus, when one or more nucleic acids are introduced into the cell, the nucleases and/or donor sequence nucleic acids may be carried on the same vector or on different vectors. When multiple vectors are used, each vector can comprise a sequence encoding a TALEN-L monomer, a TALEN-R monomer, or a donor sequence nucleic acid. Alternatively, two or more of the nucleic acids can be contained on a single vector.

Conventional viral and non-viral based gene transfer methods can be used to introduce nucleic acids encoding the nucleic acids in cells (e.g., mammalian cells) and target tissues. Non-viral vector delivery systems include DNA plasmids, naked nucleic acid, and nucleic acid complexed with a delivery vehicle such as a liposome or poloxamer. Viral vector delivery systems include DNA and RNA viruses, which have either episomal or integrated genomes after delivery to the cell. Methods of non-viral delivery of nucleic acids include electroporation, lipofection, microinjection, biolistics, virosomes, liposomes, immunoliposomes, polycation or lipid:nucleic acid conjugates, naked DNA, artificial virions, and agent-enhanced uptake of DNA. Sonoporation using, e.g., the Sonitron 2000 system (Rich-Mar) can also be used for delivery of nucleic acids.

Additional exemplary nucleic acid delivery systems include those provided by Amaxa Biosystems (Cologne, Germany), Maxcyte, Inc. (Rockville, Md.), BTX Molecular Delivery Systems (Holliston, Mass.) and Copernicus Therapeutics Inc, (see for example U.S. Pat. No. 6,008,336). Lipofection is described in e.g., U.S. Pat. Nos. 5,049,386; 4,946,787; and 4,897,355) and lipofection reagents are sold commercially {e.g., Transfectam™ and Lipofectin™). Cationic and neutral lipids that are suitable for efficient receptor-recognition lipofection of polynucleotides include those of Feigner, WO 91/17424, WO 91/16024.

The preparation of lipid:nucleic acid complexes, including targeted liposomes such as immunolipid complexes, is well known to one of skill in the art (see, e.g., Crystal, Science 270:404-410 (1995); Blaese et al, Cancer Gene Ther. 2:291-297 (1995); Behr et al, Bioconjugate Chem. 5:382-389 (1994); Remy et al, Bioconjugate Chem. 5:647-654 (1994); Gao et al, Gene Therapy 2:710-722 (1995); Ahmad et al, Cancer Res. 52:4817-4820 (1992); U.S. Pat. Nos. 4,186,183, 4,217,344, 4,235,871, 4,261,975, 4,485,054, 4,501,728, 4,774,085, 4,837,028, and 4,946,787).

Additional methods of delivery include the use of packaging the nucleic acids to be delivered into EnGeneIC delivery vehicles (EDVs). These EDVs are specifically delivered to target tissues using bispecific antibodies where one arm of the antibody has specificity for the target tissue and the other has specificity for the EDV. The antibody brings the EDVs to the target cell surface and then the EDV is brought into the cell by endocytosis. Once in the cell, the contents are released (see MacDiarmid et al (2009) Nature Biotechnology 27(7):643).

The use of RNA or DNA viral based systems for the delivery of nucleic acids take advantage of highly evolved processes for targeting a virus to specific cells in the body and trafficking the viral payload to the nucleus. Viral vectors can be administered directly to patients (in vivo) or they can be used to treat cells in vitro and the modified cells are administered to patients (ex vivo). Conventional viral based systems for the delivery of nucleic acids include, but are not limited to, retroviral, lentivirus, adenoviral, adeno-associated, vaccinia and herpes simplex virus vectors for gene transfer.

The tropism of a retrovirus can be altered by incorporating foreign envelope proteins, expanding the potential target population of target cells. Lentiviral vectors are retroviral vectors that are able to transduce or infect non-dividing cells and typically produce high viral titers. Selection of a retroviral gene transfer system depends on the target tissue. Retroviral vectors are comprised of cz's-acting long terminal repeats with packaging capacity for up to 6-10 kb of foreign sequence. The minimum cz's-acting LTRs are sufficient for replication and packaging of the vectors, which are then used to integrate the therapeutic gene into the target cell to provide permanent transgene expression. Widely used retroviral vectors include those based upon murine leukemia virus (MuLV), gibbon ape leukemia virus (GaLV), Simian Immunodeficiency virus (SIV), human immunodeficiency virus (HIV), and combinations thereof (see, e.g., Buchscher et al, J. Virol. 66:2731-2739 (1992); Johann et al, J. Virol. 66:1635-1640 (1992); Sommerfelt et al., Virol. 176:58-59 (1990); Wilson et al, J. Virol. 63:2374-2378 (1989); Miller et al, J. Virol. 65:2220-2224 (1991); PCT US94/05700).

In applications in which transient expression is preferred, adenoviral based systems can be used. Adenoviral based vectors are capable of very high transduction efficiency in many cell types and do not require cell division. With such vectors, high titer and high levels of expression have been obtained. This vector can be produced in large quantities in a relatively simple system. Adeno-associated virus (“AAV”) vectors are also used to transduce cells with target nucleic acids, e.g., in the in vitro production of nucleic acids and peptides, and for in vivo and ex vivo gene therapy procedures (see, e.g., West et al, Virology 160:38-47 (1987); U.S. Pat. No. 4,797,368; WO 93/24641; Kotin, Human Gene Therapy 5:793-801 (1994); Muzyczka, J. Clin. Invest. 94:1351 (1994). Construction of recombinant AAV vectors is described in a number of publications, including U.S. Pat. No. 5,173,414; Tratschin et al, Mol Cell. Biol. 5:3251-3260 (1985); Tratschin, et al, Mol. Cell. Biol. 4:2072-2081 (1984); Hermonat & Muzyczka, PNAS 81:6466-6470 (1984); and Samulski et al, J. Virol. 63:03822-3828 (1989).

At least six viral vector approaches are currently available for gene transfer in clinical trials, which utilize approaches that involve complementation of defective vectors by genes inserted into helper cell lines to generate the transducing agent. pLASN and MFG-S are examples of retroviral vectors that have been used in clinical trials (Dunbar et al, Blood 85:3048-305 (1995); Kohn et al, Nat. Med. 1 :1017-102 (1995); Malech et al, PNAS 94:22 12133-12138 (1997)). PA317/pLASN was the first therapeutic vector used in a gene therapy trial. (Blaese et al, Science 270:475-480 (1995)). Transduction efficiencies of 50% or greater have been observed for MFG-S packaged vectors. (Ellem et al, Immunol Immunother. 44(1):10-20 (1997); Dranoff et al, Hum. Gene Ther. 1 :111-2 (1997). Recombinant adeno-associated virus vectors (rAAV) are an alternative gene delivery systems based on the defective and nonpathogenic parvovirus adeno-associated type 2 virus. All vectors are derived from a plasmid that retains only the AAV 145 bp inverted terminal repeats flanking the transgene expression cassette. Efficient gene transfer and stable transgene delivery due to integration into the genomes of the transduced cell are key features for this vector system. (Wagner et al, Lancet 351: 9117 1702-3 (1998), Kearns et al, Gene Ther. 9:748-55 (1996)). Other AAV serotypes, including AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9 and AAVrh.10 and any novel AAV serotype can also be used in accordance with the present invention. In a particular embodiment, the vector is based on a hepatotropic adeno-associated virus vector, serotype 8 (see, e.g., Nathwani et al., Adeno-associated viral vector mediated gene transfer for hemophilia B, Blood 118(21):4-5, 2011).

Replication-deficient recombinant adenoviral vectors (Ad) can be produced at high titer and readily infect a number of different cell types. Most adenovirus vectors are engineered such that a transgene replaces the Ad El a, El b, and/or E3 genes; subsequently the replication defective vector is propagated in human 293 cells that supply deleted gene function in trans. Ad vectors can transduce multiple types of tissues in vivo, including non-dividing, differentiated cells such as those found in liver, kidney and muscle. Conventional Ad vectors have a large carrying capacity. An example of the use of an Ad vector in a clinical trial involved polynucleotide therapy for antitumor immunization with intramuscular injection (Sterman et al, Hum. Gene Ther. 7:1083-9 (1998)). Additional examples of the use of adenovirus vectors for gene transfer in clinical trials include Rosenecker et ah, Infection 24:1 5-10 (1996); Sterman et ah, Hum. Gene Ther. 9:7 1083-1089 (1998); Welsh et ah, Hum. Gene Ther. 2:205-18 (1995); Alvarez et al, Hum. Gene Ther. 5:597-613 (1997); Topf et al, Gene Ther. 5:507-513 (1998); Sterman et al, Hum. Gene Ther. 7:1083-1089 (1998).

Packaging cells are used to form virus particles that are capable of infecting a host cell. Such cells include 293 cells, which package adenovirus, and ψ2 cells or PA317 cells, which package retrovirus. Viral vectors used in gene therapy are usually generated by a producer cell line that packages a nucleic acid vector into a viral particle. The vectors typically contain the minimal viral sequences required for packaging and subsequent integration into a host (if applicable), other viral sequences being replaced by an expression cassette encoding the protein to be expressed. The missing viral functions are supplied in trans by the packaging cell line. For example, AAV vectors used in gene therapy typically only possess inverted terminal repeat (ITR) sequences from the AAV genome which are required for packaging and integration into the host genome. Viral DNA is packaged in a cell line, which contains a helper plasmid encoding the other AAV genes, namely rep and cap, but lacking ITR sequences. The cell line is also infected with adenovirus as a helper. The helper virus promotes replication of the AAV vector and expression of AAV genes from the helper plasmid. The helper plasmid is not packaged in significant amounts due to a lack of ITR sequences. Contamination with adenovirus can be reduced by, e.g., heat treatment to which adenovirus is more sensitive than AAV.

In many applications, it is desirable that the g vector be delivered with a high degree of specificity to a particular tissue type. Accordingly, a viral vector can be modified to have specificity for a given cell type by expressing a ligand as a fusion protein with a viral coat protein on the outer surface of the virus. The ligand is chosen to have affinity for a receptor known to be present on the cell type of interest. For example, Han et ah, Proc. Natl. Acad. Sci. USA 92:9747-9751 (1995), reported that Moloney murine leukemia virus can be modified to express human heregulin fused to gp70, and the recombinant virus infects certain human breast cancer cells expressing human epidermal growth factor receptor. This can be used with other virus-target cell pairs, in which the target cell expresses a receptor and the virus expresses a fusion protein comprising a ligand for the cell-surface receptor. For example, filamentous phage can be engineered to display antibody fragments (e.g., FAB or Fv) having specific binding affinity for virtually any chosen cellular receptor. Although the above description applies primarily to viral vectors, the same principles can be applied to non-viral vectors. Such vectors can be engineered to contain specific uptake sequences which favor uptake by specific target cells.

Vectors can be delivered in vivo by administration to an individual patient, typically by systemic administration (e.g., intravenous, intraperitoneal, intramuscular, subdermal, or intracranial infusion) or topical application, as described below. Alternatively, vectors can be delivered to cells ex vivo, such as cells explanted from an individual patient (e.g., lymphocytes, bone marrow aspirates, tissue biopsy) or universal donor hematopoietic stem cells, followed by re-implantation of the cells into a patient, usually after selection for cells which have incorporated the vector.

Vectors (e.g., retroviruses, adenoviruses, liposomes, etc.) containing the nucleic acids described herein can also be administered directly to an organism for transduction of cells in vivo. Alternatively, naked DNA can be administered.

Administration is by any of the routes normally used for introducing a molecule into ultimate contact with blood or tissue cells including, but not limited to, injection, infusion, topical application and electroporation. Suitable methods of administering such nucleic acids are available and well known to those of skill in the art, and, although more than one route can be used to administer a particular composition, a particular route can often provide a more immediate and more effective reaction than another route.

Vectors suitable for introduction of the nucleic acids described herein include non-integrating lentivirus vectors (IDLV). See, for example, Ory et al. (1996) Proc. Natl. Acad. Sci. USA 93:11382-11388; Dull et al. (1998) J. Virol. 72:8463-8471; Zuffery et al. (1998) J. Virol. 72:9873-9880; Follenzi et al. (2000) Nature Genetics 25:217-222; U.S. Patent Publication No 2009/054985.

The nucleic acids encoding the TALEN-L left monomer and TALEN-R right monomer can be expressed either on separate expression constructs or vectors, or can be linked in one open reading frame. Expression of the nuclease can be under the control of a constitutive promoter or an inducible promoter.

Administration can be by any means in which the polynucleotides are delivered to the desired target cells. For example, both in vivo and ex vivo methods are contemplated. In one embodiment, the nucleic acids are introduced into a subject's cells that have been explanted from the subject, and reintroduced following F8 gene repair.

For in vivo administration, intravenous injection of the nucleic acids to the portal vein is a preferred method of administration. Other in vivo administration modes include, for example, direct injection into the lobes of the liver or the biliary duct and intravenous injection distal to the liver, including through the hepatic artery, direct injection in to the liver parenchyma, injection via the hepatic artery, and/or retrograde injection through the biliary tree Ex vivo modes of administration include transduction in vitro of resected hepatocytes or other cells of the liver, followed by infusion of the transduced, resected hepatocytes back into the portal vasculature, liver parenchyma or biliary tree of the human patient, see e.g., Grossman et ah, (1994) Nature Genetics, 6:335-341.

If ex vivo methods are employed, cells or tissues can be removed and maintained outside the body according to standard protocols well known in the art. The compositions can be introduced into the cells via any gene transfer mechanism as described above, such as, for example, calcium phosphate mediated gene delivery, electroporation, microinjection, proteoliposomes, or viral vector delivery. The transduced cells can then be infused (e.g., in a pharmaceutically acceptable carrier) or homotopically transplanted back into the subject per standard methods for the cell or tissue type. Standard methods are known for transplantation or infusion of various cells into a subject.

7. Immune Tolerance Induction

In one embodiment, the repaired gene, upon expression, provides for the induction of immune tolerance to an administered replacement FVIII protein product. Current FVIII replacement therapies include the infusions of recombinant FVIII replacement products (r)FVIII. (r)FVIII is a biosynthetic blood coagulation prepared using recombinant DNA, and is structurally similar to endogenous wild-type human FVIII and produces the same biological effect. Due to genetic variables within a subject including the individual's specific F8 mutation type, background FVIII haplotype, and HLA haplotype, however, the (r)FVIII mismatched amino acid may induce an immune response in the subject receiving the (r)FVIII, resulting in the development of inhibitors and the reduction in efficiency of the particular (r)FVIII.

Accordingly, in one embodiment, a method of inducing tolerance to a (r)FVIII product in a subject that may receive, is receiving, or has received a (r)FVIII product is provided comprising introducing into a cell of the subject one or more isolated nucleic acids encoding a nuclease that targets a portion of the human F8 gene containing a mutation that causes hemophilia A, wherein the nuclease creates a double stranded break in the human F8 gene; and an isolated nucleic acid comprising (i) a nucleic acid encoding a truncated FVIII polypeptide or (ii) a native F8 3′ splice acceptor site operably linked to a nucleic acid encoding a truncated FVIII polypeptide, wherein the nucleic acid comprising the (i) a nucleic acid encoding a truncated FVIII polypeptide or (ii) native F8 3′ splice acceptor site operably linked to a nucleic acid encoding a truncated FVIII polypeptide is flanked by nucleic acid sequences homologous to the nucleic acid sequences upstream and downstream of the double stranded break in the DNA, and wherein the repaired gene, upon expression, provides for the induction of immune tolerance to an administered replacement FVIII protein product. The person administered the cells in which the F8 gene has been repaired may or may not have anti-FVIII antibodies as measured by ELISA or Bethesda assays. In one embodiment, the truncated FVIII polypeptide amino acid sequence shares homology with a positionally coordinated portion of the (r)FVIII amino acid sequence. In one embodiment, the truncated FVIII polypeptide amino acid sequence shares complete homology with a positionally correlated portion of the (r)FVIII amino acid sequence. In a further embodiment, the method further includes targeting and replacing a nucleic acid sequence within the subject's F8 gene encoding a non-mutational amino acid with the positional equivalent amino acid in the (r)FVIII. In one embodiment, the non-mutational amino acid is a non-synonymous Single Nucleotide Polymorphism (ns-SNP).

It is believed that intra-cellular expression of even a small amount of a repaired FVIII protein that closely resembles the (r)FVIII product, and concomitant surface presentation of FVIII epitopes within the cell's MHC, may enable the induce of immune tolerance to the (r)FVIII products.

The human F8 gene is polymorphic and encodes several structurally distinct FVIII proteins referred to as haplotypes. Sequencing studies of the F8 gene have revealed four common nonsynonymous-single-nucleotide polymorphisms (nsSNPs) that, together with two infrequent ns-SNPs, encode eight distinct wild-type FVIII proteins referred to as haplotype H1, H2, H3, H4, H5, H6, H7, and H8. The amino acid sequence of the H1 wild-type variant is listed as Seq. ID. No. 16.

All currently available (r)FVIII are based on either the H1 or H2 haplotype variant. Commercially available (r)FVIII include the H1 variants Kogenate® (Bayer) and Helixate® (ZLB Behring), the H2 variants Recombinate® (Baxter) and Advate® (Baxter), and the H1/H2 variant B-domain deleted Refacto® (Pfizer) and Xyntha® (Pfizer). The present invention, however, is not limited to replacing a subject's F8 gene with a coding sequence that matches or is nearly homologous to a portion of the commercially available (r)FVIII products described above, but is applicable to any (r)FVIII, including human/porcine hybrid (r)FVIII, porcine (r)FVIII, and alternative haplotype recombinant FVIII replacement products such as those identified in WO 2006/063031, which is incorporated by reference herein. Differences between a subject's FVIII and a (r)FVIII can result from, for example, missense mutations in the subject's F8 gene, nonsynonymous single-nucleotide polymorphisms (nsSNPs) (both well-known and “private” or individualized) or haplotypic variations between the subject's FVIII and (r)FVIII, inversions, for example intron 1 or 22 inversions, synthetic peptide inclusion due to B-domain deletions in the BDD-®FVIII, and the like.

Because the amino acid sequence of available (r)FVIII are known, and differences in subject's FVIII can be determined, differences (or mismatches) between the subject's endogenous FVIII protein sequence and (r)FVIII can be readily identifiable using common techniques known in the art, and the identified differences can be utilized to construct nucleic acids as described above for replacement. For example, molecular genetic studies have shown that development of inhibitors to factor VIII replacement products occurs most frequently in patients with severe hemophilia due to major gene lesions including inversions. Subjects with intron 22 inversion express the entire FVIII intracellularly, albeit on two separate polypeptides. Importantly, another gene, F8B, is also generally expressed in both normal and HA subjects. The expression product of the F8B gene, FVIIIB, has sequence identity with a portion of the C1 domain and the entire C2 domain of FVIII. The presence of this FVIIIB polypeptide is important from a tolerance standpoint as it serves as a source for any T cells epitope or B cell epitopes needed to support processes that occur in the thymus (T cell clonal deletion) and spleen (B cell anergy) to achieve central tolerance. The expression product of F8I22I starts at residue 1 and ends at residue 2124. The polypeptide expressed by the F8B begins at residue 2125 and ends at residue 2332. Accordingly subjects having the F8I22I have the requisite FVIII material to yield one or more FVIII peptides ending at or before residue 2124, the last amino acid encoded by exon 22, or beginning at or after residue 2125, the first amino acid encoded by exon 23. Any T cell epitope within such a peptide can be recognized as a self-antigen and not be immunogenic in the subject. Peptides spanning the junction between residues 2124 and 2125, if proteolyzed from a (r)FVIII and presented by MHC class II molecules, however, are “foreign” and potentially immunogenic T cell epitopes in an F8I22I subject. Because of this, all subjects having F8I22I have similar reference.

Likewise, in subjects receiving B-domain deleted-(r)FVIII product, differing amino acid sequence exist between the subject's FVIII and the replacement product caused by the removal of the B-domain in the BDD-rFVIII product. For example, in certain BDD-rFVIII, a deletion of 894 internal codons and splicing codons 762 and 1657 creates a FVIII product containing 1438 amino acids. The BDD-rFVIII contains a synthetic junctional 14-peptide sequence SFS-QNPPVLKRHQR formed by covalent attachment of the three N-terminal most residues of the B-domain, S⁷⁴¹F⁷⁴²S⁷⁴³, to the 11 C-terminal-most residues Q¹⁶³⁸N¹⁶³⁹P¹⁶⁴⁰P¹⁶⁴¹V¹⁶⁴²L¹⁶⁴³K¹⁶⁴⁴R¹⁶⁴⁵H¹⁶⁴⁶Q¹⁶⁴⁷R¹⁶⁴⁸. This synthetic linker creates 11 unique peptides across a 15 amino acid sequence within the BDD-rFVIII, which have potential immunogenicity. In one embodiment, a donor sequence including these amino acids is utilized to replace the subject's F8 gene. Thus, in one embodiment, a donor sequence comprising a nucleic acid encoding the amino acid sequence SFSQNPPVLKRHQR is provided. In alternative embodiments, the BDD-rFVIII contains variable amounts of linker sequences. In one embodiment, the linker sequence comprises the first 10 amino acids from the N-terminus of the B-domain and 11 amino acids from the C-terminus of the B-domain.

In one embodiment, a F8 mutation in a cell from a subject having HA, for example a BOEC, iPSC, or LSEC, is identified and repaired using the nuclease approach described above and a donor sequence that is identical to a portion of a (r)FVIII product. In one embodiment, the repair takes place ex vivo, as a cell, for example a BOEC or LSEC, is explanted from the subject, repaired, and reintroduced into the subject as described above. Following repair, the cell is capable of producing FVIII, including intracellularly, and express and present potentially antigenic peptides on MHC complexes. The expression of the repaired FVIII leads to immune suppression specific to a specific (r)FVIII antigen or immunogenic epitopes expressed by the repaired F8 gene. Such a tolerogenic immune response can include any reduction, delay, or inhibition in an undesired immune response specific to the (r)FVIII antigen or epitope. Tolerogenic immune responses, therefore, can include the prevention of or reduction in inhibitors to a specific (r)FVIII. Tolerogenic immune responses as provided herein include immunological tolerance. The tolerogenic immune response can be the result of MHC Class II-restricted presentation and/or B cell presentation, or any other presentation leading to the minimized or reduced immunicity of the (r)FVIII.

Tolerogenic immune responses include a reduction in (r)FVIII antigen-specific antibody (inhibitor) production. The expression of the repaired FVIII can result in a reduction of measurable Bethesda titer units to a (r)FVIII in a subject that already has inhibitors to a (r)FVIII. Tolerogenic immune responses also include any response that leads to the stimulation, production, or recruitment of CD4+ Treg cells and/or CD8+ Treg cells. CD4+ Treg cells can express the transcription factor FoxP3 and inhibit inflammatory responses and auto-immune inflammatory diseases (Human regulatory T cells in autoimmune diseases. Cvetanovich G L, Hafler D A. Curr Opin Immunol. 2010 December; 22(6):753-60. Regulatory T cells and autoimmunity. Vila J, Isaacs J D, Anderson A E. Curr Opin Hematol. 2009 July; 16(4):274-9). Such cells also suppress T-cell help to B-cells and induce tolerance to both self and foreign antigens (Therapeutic approaches to allergy and autoimmunity based on FoxP3+ regulatory T-cell activation and expansion. Miyara M, Wing K, Sakaguchi S. J Allergy Clin Immunol. 2009 April; 123(4):749-55). C D4+ Treg cells recognize antigen when presented by Class II proteins on APCs. CD8+ Treg cells, which recognize antigens presented by Class I (and Qa-1), can also suppress T-cell help to B-cells and result in activation of antigen-specific suppression inducing tolerance to both self and foreign antigens. Disruption of the interaction of Qa-1 with CD8+ Treg cells has been shown to dysregulate immune responses and results in the development of auto-antibody formation and an auto-immune lethal systemic-lupus-erythematosus (Kim et al., Nature. 2010 Sep. 16, 467 (7313): 328-32). CD8+ Treg cells have also been shown to inhibit models of autoimmune inflammatory diseases including rheumatoid arthritis and colitis (CD4+CD25+regulatory T cells in autoimmune arthritis. Oh S, Rankin A L, Caton A J. Immunol. Rev. 2010 January; 233(1):97-111. Regulatory T cells in inflammatory bowel disease. Boden E K, Snapper S B. Curr Opin Gastroenterol. 2008 November; 24(6):733-41). In some embodiments, the expression of the repaired FVIII provided can effectively result in both types of responses (CD4+ Treg and CD8+ Treg). In other embodiments, FoxP3 can be induced in other immune cells, such as macrophages, iNKT cells, etc., and the compositions provided herein can result in one or more of these responses as well.

Tolerogenic immune responses also include, but are not limited to, the induction of regulatory cytokines, such as Treg cytokines; induction of inhibitory cytokines; the inhibition of inflammatory cytokines (e.g., IL-4, IL-1b, IL-5, TNF-α, IL-6, GM-CSF, IFN-γ, IL-2, IL-9, IL-12, IL-17, IL-18, IL-21, IL-22, IL-23, M-CSF, C reactive protein, acute phase protein, chemokines (e.g., MCP-1, RANTES, MIP-1α, MIP-1β, MIG, ITAC or IP-10), the production of anti-inflammatory cytokines (e.g., IL-4, IL-13, IL-10, etc.), chemokines (e.g., CCL-2, CXCL8), proteases (e.g., MMP-3, MMP-9), leukotrienes (e.g., CysLT-1, CysLT-2), prostaglandins (e.g., PGE2) or histamines; the inhibition of polarization to a Th17, Th1, or Th2 immune response; the inhibition of effector cell-specific cytokines: Th17 (e.g., IL-17, IL-25), Th1 (IFN-γ), Th2 (e.g., IL-4, IL-13); the inhibition of Th1-, Th2- or TH17-specific transcription factors; the inhibition of proliferation of effector T cells; the induction of apoptosis of effector T cells; the induction of tolerogenic dendritic cell-specific genes, the induction of FoxP3 expression, the inhibition of IgE induction or IgE-mediated immune responses; the inhibition of antibody responses (e.g., antigen-specific antibody production); the inhibition of T helper cell response; the production of TGF-β and/or IL-10; the inhibition of effector function of autoantibodies (e g , inhibition in the depletion of cells, cell or tissue damage or complement activation); etc.

Any of the foregoing can be measured in vivo or may be measured in vitro. One of ordinary skill in the art is familiar with such in vivo or in vitro measurements. Tolerogenic immune responses can be monitored using, for example, methods of assessing immune cell number and/or function, tetramer analysis, ELISPOT, flow cytometry-based analysis of cytokine expression, cytokine secretion, cytokine expression profiling, gene expression profiling, protein expression profiling, analysis of cell surface markers, PCR-based detection of immune cell receptor gene usage (see T. Clay et al., “Assays for Monitoring Cellular Immune Response to Active Immunotherapy of Cancer” Clinical Cancer Research 7:1127-1135 (2001)), etc. Tolerogenic immune responses may also be monitored using, for example, methods of assessing protein levels in plasma or serum, immune cell proliferation and/or functional assays, etc. In some embodiments, tolerogenic immune responses can be monitored by assessing the induction of FoxP3.

In some embodiments, the reduction of an undesired immune response or generation of a tolerogenic immune response may be assessed by determining clinical endpoints, clinical efficacy, clinical symptoms, disease biomarkers and/or clinical scores. Tolerogenic immune responses can also be assessed with diagnostic tests to assess the presence or absence of inhibitors.

In one embodiment, expression of the repaired FVIII results in the prevention, reduction, or elimination of inhibitors to a (r)FVIII. The presence of inhibitors can be assessed by determining one or more antibody titers to the (r)FVIII using techniques known in the art and include Enzyme-linked Immunosorbent Assay (ELISA), inhibition liquid phase absorption assays (ILPAAs), rocket immunoelectrophoresis (RIE) assays, and line immunoelectrophoresis (LIE) assays.

In one embodiment, cells can be harvested, repaired, and then stored for future tolerance induction administration. The cells can be administered in effective amounts, such as the effective amounts described elsewhere herein. Doses of dosage forms contain varying amounts of cells expressing a repaired FVIII, according to the invention. The amount of expressing cells present in the dosage forms can be varied according to the nature and amount of the expressed FVIII, the therapeutic benefit to be accomplished, and other such parameters. In embodiments, dose ranging studies can be conducted to establish optimal therapeutic amount of repaired FVIII peptides to be expressed by the cells. In embodiments, the cells express a repaired FVIII in a dosage form in an amount effective to generate a tolerogenic immune response to a (r)FVIII epitope upon administration to a subject. It may be possible to determine amounts of cellular expression effective to generate a tolerogenic immune response using conventional dose ranging studies and techniques in subjects. Dosage forms may be administered at a variety of frequencies. In one embodiment, at least one administration of expressing cells is sufficient to generate a pharmacologically relevant response. In one embodiment, at least two administrations, at least three administrations, or at least four administrations or more, of the expressing cells are utilized to ensure a pharmacologically relevant response.

Prophylactic administration of the expressing cells can be initiated prior to the onset of inhibitor development, or therapeutic administration can be initiated after inhibitor development is established. In some embodiments, administration of cells expressing repaired FVIII is undertaken e.g., prior to administration of the (r)FVIII. In exemplary embodiments, the expressing cells are administered at one or more times including, but not limited to, 30, 25, 20, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, or 0 days prior to administration of the (r)FVIII. In addition or alternatively, the cells can be administered to a subject following administration of the (r)FVIII. In exemplary embodiments, cells are administered at one or more times including, but not limited to, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, etc. days following administration of (r)FVIII.

In some embodiments, a maintenance dose is administered to a subject after an initial administration has resulted in a tolerogenic response in the subject, for example to maintain the tolerogenic effect achieved after the initial dose, to prevent an undesired immune reaction in the subject, or to prevent the subject becoming a subject at risk of experiencing an undesired immune response or an undesired level of an immune response. In some embodiments, the maintenance dose is the same dose as the initial dose the subject received. In some embodiments, the maintenance dose is a lower dose than the initial dose. For example, in some embodiments, the maintenance dose is about ¾, about ⅔, about ½, about ⅓, about ¼, about ⅛, about 1/10, about 1/20, about 1/25, about 1/50, about 1/100, about 1/1,000, about 1/10,000, about 1/100,000, or about 1/1,000,000 (weight/weight) of the initial dose.

In some aspects, methods and compositions provided herein are useful in conjunction with established means of ITI for (r)FVIII. ITI protocols for hemophilia patients, including patients with high titer inhibitors against (r)FVIII, are known in the art and are generally described, e.g., in Mariani et al., Thromb Haemost., 72: 155-158 (1994) and DiMichele et al., Thromb Haemost. Suppl 130 (1999). Administration of the repaired cells described herein can be conducted before, after, and/or concurrently with established ITI protocols and/or variations thereof. For example, in some aspects, methods provide herein increase the effectiveness of established ITI protocols (e.g., the degree and/or likelihood of successful treatment) and/or reduce associated costs or side effects. In further aspects, methods provide herein allow established ITI protocols to be beneficially modified, e.g., to decrease the frequency, duration, and/or dose of FVIII administration.

In a particular embodiment, the ITI strategy described herein is combined with an antigenic peptide immunization strategy. In a particular embodiment, the strategy described herein is combined with the administration of overlapping sets of tolerogenic peptides based on amino acid differences between the (r)FVIII protein and the subject's endogenous FVIII protein. In a particular embodiment, the strategy described herein is combined with the administration of overlapping sets of tolerogenic peptides based on amino acid differences between the (r)FVIII protein and the subject's repaired FVIII protein, described in U.S. Application 61/802,547, incorporated by reference herein. These amino acid residue differences between the subject's FVIII and (r)FVIII can be positioned or mapped within specific loci in the (r)FVIII, wherein the differing (r)FVIII amino acids—individually termed the reference locus—serves as a reference point or points for the preparation of a set or sets of tolerizing peptides—termed tolerizing amino acids (“TAAs”)—that may incorporate T-cell epitopes capable of inducing immune tolerance of, or the prevention, reduction, or elimination of inhibitor development to, the (r)FVIII. Each TAA within a set includes a (r)FVIII amino acid residing at a reference locus, and a TAA set includes between about 9 to 21 separate peptides of between 9 to 21 amino acids in length, wherein the number of peptides in a TAA set is directly correlated with the amino acid length of the TAA (i.e., a TAA set containing TAAs 9 amino acids in length contains 9 peptides; a TAA set containing TAAs 10 amino acids in length contains 10 peptides, etc.).

A method of deriving TAA peptides is generally as follows. The first peptide of each TAA has as its first amino acid position the first amino acid residue of a reference locus of the (r)FVIII, while the remaining amino acid residues are identical to the downstream amino acids in the (r)FVIII across the length of the TAA peptide. If only a single amino acid residue difference exists at the locus (for example in the case of a missense mutation or nsSNP), then the reference locus consists of a single amino acid residue. If the differences encompass more than one contiguous amino acid residue (for example in the case of some deletions), then the first differing amino acid residue in the (r)FVIII serves as the reference locus. For example, if the TAA is 9 amino acids in length, the first amino acid in the first peptide is the first amino acid of the reference locus, and the remaining 8 amino acid residues are the 8 loci residues of the (r)FVIII immediately downstream from the reference locus (as determined from amino acid position 1 to 2332 in the wt FVIII protein). The second peptide of each TAA has as its second amino acid position the reference locus, with the first amino acid position being the first amino acid residue in the (r)FVIII immediately upstream from the reference locus, and the remaining 7 amino acid residues being the 7 loci residues of the (r)FVIII immediately downstream from the reference locus. As such, for each successive TAA peptide in the TAA set, the reference locus is shifted one amino acid position downstream, and the first amino acid reflects a shift from the preceding peptide of one amino acid upstream in the (r)FVIII. Accordingly, the last TAA peptide of the set—in the preceding example, the ninth peptide—has the reference locus in the last amino acid residue position, and be preceded by upstream amino acid residues—in the preceding example, the 8 residues of the (r)FVIII immediately upstream of the reference locus. The same method described above can be generally used to create TAA sets of varying peptide sizes, wherein the reference locus in each successive peptide in the set is shifted one position downstream and the first amino acid position in each successive peptide is shifted one residue upstream from the first amino acid position in the preceding peptide, until the reference locus occupies the last amino acid position in the last peptide of the set.

Following the method of generating sets of TAA as described above, a set of TAA peptides corresponds with a contiguous portion of the (r)FVIII across 2X−1 amino acids, where X is the length of the peptides contained in the set. For example, as described in the preceding example, a TAA set containing 9 peptides, each being 9 amino acids in length, will as a set overlap with 17 contiguous amino acids of the (r)FVIII. Furthermore, the contiguous (r)FVIII amino acid sequence overlapped by the TAA peptides includes X−1 amino acid residues upstream and X−1 amino acid residues downstream from the first amino acid of the reference locus within the (r)FVIII, wherein X is the length of the peptides contained in the set. For example, a set of 9 peptides of 9 amino acids in length overlaps with 8 amino acids upstream and 8 amino acids downstream from the first amino acid of the reference locus within the (r)FVIII. This general process will be applicable to the generation of TAA sets for most identified amino acid differences, with a few exceptions, for example in the derivation of TAA sets to a few BDD-rFVIIIrp synthetic linker as described further herein.

In an alternative embodiment, the present strategy is combined with methods of antigen specific muting of the B cell response to specific potential antigens within the (r)FVIII. Accordingly, the repaired cells are combined with a strategy using liposomal nanoparticles displaying peptides comprising peptides derived from the (r)FVIII and based on amino-acid mismatches between the subject's endogenous FVIII protein, or alternatively the repair FVIII protein, and the (r)FVIII (as described above), and glycan ligands of the inhibitory co-receptor CD22. Methods of producing antigenic liposomes displaying CD22 ligands are described in, for example, Macauley et al., “Antigenic liposomes displaying CD22 ligands induce antigen-specific B cell apoptosis,” J. Clin. Invest. 2013 Jul. 1, 123(7): 3074-3083.

In some embodiments, the cells are associated with, combined with, or administered with immunosuppressive compounds capable of inducing adaptive regulatory T cells. In one embodiment, the immunosuppresive compounds may include, but is not limited to, IL-10, TGF-β, and/or rapamycin and/or other limus compounds, including but not limited to biolimus A9, everolimus, tacrolimus, and zotarolimus, and/or combinations thereof.

In one embodiment a “dose escalation” protocol can be followed, where a plurality of doses is given to the patient in ascending concentrations. Such an approach has been used, for example, for phospholipase A2 peptides in immunotherapeutic applications against bee venom allergy (Müller et al. (1998) J. Allergy Clin Immunol. 101:747-754 and Akdis et al. (1998) J. Clin. Invest. 102:98-106).

In one aspect, the amount of cells to be administered can be determined using a stoichiometric calculation based on current ITI administration protocols. For example, the amount of cells to be administered can be based on the equivalent quantity of the peptide that would be administered in a standard ITI protocol which uses the full length (r)FVIII. To determine dosing period, the subject's dendritic cells' reactivity to the expressed repaired FVIII can be determined prior to the start of cell administration, and then periodically monitored until tolerance to the (r)FVIII is observed.

EXAMPLES Example 1 Ex Vivo Gene Repair

Examples are provided of an ex vivo gene repair strategies that can be performed without the use of viral vectors. Genetic materials are delivered to restore secretion of a wild-type full-length FVIII protein to lymphoblastoid cells derived from a human HA patient with the intron-22 (I22)-inverted FVIII gene, designated F8_(I22I), using electroporation and TALE-nucleases (TALENs). A similar strategy can be used as an example to repair the naturally-occurring I22I-mutation in cells from an animal model of HA (dogs of the HA canine colony located at the University of North Carolina in Chapel Hill). Canine (adipose) tissue, which can be induced to acquire many properties of hepatocytes, can be used.

Use of autologous cells is an attractive therapy for several reasons as levels of blood clotting proteins needed to maintain hemostasis may be more readily produced by expansion of large populations of cells ex vivo and reintroduction into the patient. Repair of the F8I22I gene residing in a B-lymphoblastoid cell-line derived from a patient with severe HA caused by the I22I-mutation is effected by using electroporation to deliver (i) two distinct mRNAs encoding a highly specific heterodimeric TALEN that targets a single human genome site located in F8 near the 5′-end of I22 and (ii) the corresponding donor plasmid that carries the “editing cassette”, which is comprised of a functional 3′-intron splice site ligated immediately 5′ of a partial F8 cDNA matched in sequence with the wild-type sequence of exons 23-26 in the patient's own I22-inverted F8 locus, flanked by “left” and “right” homology arms.

The use of viral-free methods to derive autologous cells of various phenotypes and to stably introduce genetic information into the genome is attractive. These methods can be effectively used to successfully “repair” the intron-22 (I22)-inverted human F8 locus (F8I22I), which arises through a highly-recurrent mutational event essentially restricted to the male germ-line. This same F8 abnormality, which is widely known as the I22-inversion (I22I)-mutation, occurs naturally in dogs, and results in spontaneous bleeding. Two large colonies of HA dogs have been established, one at the University of North Carolina in Chapel Hill. Investigation of F8I22I at the molecular genetic, biochemical, and cellular levels to characterize its expression products have been studied in order to determine the immune response to replacement FVIII. Extensive sequencing efforts and analyses of the F8I22I and its mRNA transcripts allow for an innovative gene repair strategy that exploits nuclease technology, for example, transcription activator-like effector (TALE)-nuclease (TALEN) technology to repair the I22I-mutation.

Lymphoblastoid cells derived from HA patient with the I22I-mutation is obtained. The left (TALEN-L) and right (TALEN-R) monomers comprising the heterodimeric TALEN is shown in FIG. 3, which was specifically designed to cleave within the human F8 I22-sequence, ˜1 kb downstream of the 3′-end of exon-22. In alternative embodiments, the TALENs target sequences throughout the FVIII gene, with replacement of the corresponding FV8 gene sequence on the donor sequence.

An example of a sequence that can be targeted includes a sequence within intron 22 (tactatgggatgagttgcagatggcaagtaagacactggggagattaaat (SEQ. ID No. 1)), where the underlined regions of sequence are recognized by the left TAL Effector DNA-binding domain and the right TAL Effector DNA-binding domain). Another example of a sequence that can be targeted includes a sequence at the junction of exon 22 with intron 22 (tggaaccttaatggtatgtaattagtcatttaaagggaatgcctgaata (SEQ. ID No. 2)), where the underlined regions of sequence are recognized by the left TAL Effector DNA-binding domain and the right TAL Effector DNA-binding domain). Another example of a sequence that can be targeted within intron 22 is depicted in FIG. 3 (ttagtattatagtttctcagattatcaccagtgatactatggga (SEQ. ID No. 3)), where the underlined regions of sequence are recognized by the left TAL Effector DNA-binding domain and the right TAL Effector DNA-binding domain). The two TALEN expression plasmids that target these sequences (or the mRNA) are co-transfected with the donor plasmid. The donor plasmid contains flanking homology regions to the intron 22 locus, which allows for recombination of the donor plasmid into the chromosome. The cDNA of exons 23 to 26 of the F8 gene is contained between the flanking homology regions of the donor plasmid. The donor plasmid can also contain a suicide gene (such as the thymidine kinase gene from the herpes simplex virus), which allows counter-selection to avoid random and multi-copy integration into the genome.

Electroporation (AMAXA Nucleofection system) and chemical transfection (with a commercial reagent optimized to this cell type) can be used as transfection methods for the lymphoblastoid cells. A plasmid containing the green fluorescent protein (GFP) gene is introduced into the cells using both methods. The cells are analyzed by fluorescent microscopy to obtain an estimate of transfection efficiency, and the cells are observed by ordinary light microscopy to determine the health of the transfected cells. Any transfection method that gives a desirable balance of high transfection efficiency and preservation of cell health in the lymphoblastoid cells can be used. The TALEN mRNAs and the gene repair donor plasmid is then introduced into the lymphoblastoid cells using a transfection method. The TALENs for the human lymphoblastoid cells and their target site are shown in FIG. 3.

Repair of the F8I22I in the adipose tissue-derived hepatocyte-like cells from the I22I HA canine animal model is effected using electroporation to deliver mRNAs encoding an analogous TALEN that targets the 5′-end of I22 in canine F8 and an analogous donor plasmid carrying a “splice-able” cDNA spanning canine F8 exons 23-26.

Adipose tissue is collected from these FVIII deficient dogs by standard liposuction. Stromal cells from the adipose tissue are reprogrammed into induced pluripotent stem cells (iPSC), as described by Sun et al. (“Feeder-free derivation of induced pluripotent stem cells from adult human adipose stem cells” Proc Natl Acad Sci USA. 106: 720-5, 2009) with two modifications: (i) mRNA of the reprogramming factors are used in place of lentiviral vectors and (ii) the reprogramming is performed under conditions of hypoxia, 5% O2, and in the presence of small molecules that have been found to increase the reprogramming efficiency. Once produced and characterized, pluripotent canine cells are obtained.

The defective FVIII sequence in iPSC is replaced by the correct sequence using site-specific TALE nucleases (see FIG. 4). The iPSC with repaired Factor VIII are differentiated into hepatocytes using well established protocols (see, for example, Hay et al. “Direct differentiation of human embryonic stem cells to hepatocyte-like cells exhibiting functional activities” Cloning Stem Cells. 9: 51-62, 2007; Si-Tayeb et al. “Highly efficient generation of human hepatocyte-like cells from induced pluripotent stem cells” Hepatology. 51: 297-305, 2010; and Cayo et al. “JD induced pluripotent stem cell-derived hepatocytes faithfully recapitulate the pathophysiology of familial hypercholesterolemia” Hepatology. May 31, 2012). In short, small colonies of iPSC are induced to differentiate for the first 3 days into definitive endoderm by treatment with 50 ng/mL Wnt3a and 100 ng/mL Activin A, and then into the hepatocyte lineage by 20 ng/mL BMP4. Two expression plasmids necessary to produce mRNAs encoding a functional TALEN are obtained. These are designed to cleave and yield a double-stranded DNA break at only a single site within the canine genome, located within canine F8 I22, ˜0.3 kb downstream of the 3′-end of exon-22. The left (TALEN-L) and right (TALEN-R) monomers comprising this heterodimeric TALEN is shown above in FIG. 4.

A donor plasmid containing the sequence of the 3′-end of canine F8 intron-22 and all of canine F8 exon-22 as the left homologous sequence and the 5′-end of canine F8 intron-23 as the right homologous sequence to provide an adequate length of genomic DNA for efficient homologous recombination at the target site (i.e., the TALEN cut site) is created. The TALEN mRNAs and the gene repair donor plasmid are introduced into the pluripotent canine cells using a transfection method described herein.

Likewise, in humans, human iPSCs are electroporated with the human F8 TALENs & donor plasmid described above, to assess candidate genome-editing tools (which were designed to be equally capable of “editing” the I22-sequence in the wild-type and I22-inverted F8 loci, F8 and F8I22I, respectively) for their efficiency of site-specific gene repair. The genomic DNA at the repaired F8 loci, as well as the mRNAs and expression products synthesized by, the cells described above are assessed before and after electroporation.

The TALEN gene repair method described above inserts F8 exons 23-26 immediately downstream (telomeric) to F8 exons 1-22 to encode a FVIII protein. Genomic DNA, spliced mRNA, and protein sequences differ among normal, repaired, and unrepaired cells (see FIG. 5). Gene repair is verified in genomic DNA through the use of PCR. Specific PCR primers are designed to amplify across the homologous recombination target sequence in unrepaired and repaired cells. A common primer is placed toward the end of exon-22. An I22I-specific primer is placed in the sequence telomeric to exon-22 in the I22I-inverted cells. A Repaired-specific primer is placed in the inserted exon 23-26 sequence. Primer design is shown in FIG. 8. Separate sets of primers are designed for human and canine sequences.

Characterization of the genomic DNA at the repaired F8 loci, as well as the mRNAs and expression products synthesized by, the cells described above, before and after electroporation are performed.

A quantitative RT-PCR test that specifically detects and quantifies the mRNA transcripts from normal and I22I cells is used. The quantitative RT-PCR test uses three separate primer sets: one set to detect exons 1-22, one set to detect exons 23-26, and one set that spans the exon-22/exon-23 junction. mRNA is purified from cells before and after transfection. The existing primer design to probe mRNA from the human cells is used. Primers against canine sequences are designed using the same strategy and then the mRNA from the canine cells is probed using these new primers. An increased signal from the exon-22/exon-23 junction reaction in repaired cells, relative to unrepaired cells should be observed.

Monoclonal antibody ESH8, which is specific for the C2-domain of the FVIII protein, is be used. NIH3T3 cells were transfected with expression constructs encoding full-length and I22I F8 genes and then assayed by flow cytometry. Signal from the ESH8 antibody was high in cells transfected with the full-length construct but virtually absent in cells transfected with the I22I construct. The ESH8 antibody is used to test transfected cells. There should be an increased signal in repaired cells relative to unrepaired cells. Secreted FVIII levels, as measured by ELISA, are dramatically lower in I22I cells relative to normal cells. Whole-cell lysates and supernates from transfected cells are obtained and tested for FVIII concentration by ELISA. There should be an increase in FVIII concentration in the supernates from repaired cells relative to unrepaired cells.

In another example, canine blood outgrowth endothelial cells (cBOECs) and canine iPSCs derived from canine adipose tissue can be transfected with TALENs that target the F8I22I canine gene and a plasmid repair vehicle that carries exons 23-26 of cF8. TALENs are expected to make DSBs in the F8I22I DNA at the target site to allow “homologous recombination and repair” of the canine F8 I22I gene by insertion of exons 23-26 of the canine F8. The TALENS are designed to cleave and yield a DSB at only a single site within the canine genome, located within canine F8 I22, (˜0.3 kb) downstream of the 3′-end of exon-22. The donor plasmid contains the sequence of canine F8 exons 23-26 flanked by the 3′-end of canine F8 intron-22 and all of canine F8 exon-22 as the left homologous sequence and the 5′-end of canine F8 intron-23 as the right homologous sequence to provide an adequate length of genomic DNA for efficient homologous recombination at the target site.

Feasibility of deriving canine iPSCs is well established. An mRNA transcript that enables expression of the so called “Yamanaka” genes coding for transcription factors OCT4, SOX2, KLF4 and C-MYC to induce iPSCs from canine adipose derived stem cells (hADSCs). iPSCs have been transfected using Nucleofector. For transfection, Qiagen's Polyfect transfection reagents can be used with TALENs for many cell types, including BOECs. Transfection methods can be assessed using commercial reagents and transfected cells can be analyzed by fluorescent microscopy to obtain an estimate of transfection efficiency, while viability can be determined by Trypan Blue dye exclusion. The transfection method that gives the best balance of high transfection efficiency and preservation of cell health can be used.

Prior to commencing transfection with the TALENS and repair plasmid, the cleavage activity of the TALENs against the target site can be analyzed. This can be done by monitoring TALEN induced mutagenesis (Non-Homologous End Joining Repair) via a T7 Endonuclease assay. To assess potential risk of unintended genomic modification induced by the selected repair method, off-site activity is analyzed following transfection. In silico identification based on homologous regions within the genome can be used to identify the top 20 alternative target sites containing up to two mismatches per target half-site. PCR primers can be synthesized for the top 20 alternative sites and Surveyor Nuclease (Cel-I) assays (Transgenomics, Inc.) can be performed for each potential off-target site.

Transfection for expression and secretion of FVIII can be assessed in the various cell types before and after transfection. Genomic DNA is isolated from cells before and after transfection. Purified genomic DNA is used as template for PCR. Primers are designed for amplification from a FVIII I22I-specific primer only in unrepaired cells, and amplification from the repaired-specific primer only in repaired cells. RT-PCR can specifically detect and quantify the mRNA hF8 transcripts from normal and I22I cells. The quantitative RT-PCR test uses three separate primer sets: one set to detect exons 1-22, one set to detect exons 23-26, and one set that spans the exon-22/exon-23 junction. mRNA is purified from cells before and after transfection, with an increased signal from the exon-22/exon-23 junction reaction in repaired cells, relative to unrepaired cells. Flow-cytometry based assays may also be used for FVIII protein in peripheral blood mononuclear cells (PBMCs).

iPSCs derived from canine adipose tissue engineered can be conditioned to secrete FVIII to hepatocyte-like tissue. Canine iPSCs are conditioned toward hepatocyte like cells using a three step protocol as described by Chen et al. that incorporates hepatocyte growth factor (HGF) in the endodermal induction step (Chen Y F, Tseng C Y, Wang H W, Kuo H C, Yang V W, Lee O K. Rapid generation of mature hepatocyte-like cells from human induced pluripotent stem cells by an efficient three-step protocol. Hepatology. 2012 April; 55(4):1193-203).

Subpopulations of cBOECs are segregated and expanded and then characterized for the expression of endothelial markers, such as Matrix Metalloproteinases (MMPs), and cell-adhesion molecules (JAM-B, JAM-C, Claudin 3, and Claudin 5) using RT-PCR. Detailed RT-PCR methods, including primers for detecting expression of mRNA transcripts of the cell-adhesion molecules of interest and detailed immunohistochemistry methods to detect the proteins of interest, including a list of high affinity antibodies have been published by Geraud et al. (Géraud C, et al. Unique cell type-specific junctional complexes in vascular endothelium of human and rat liver sinusoids. PLoS One. 2012; 7(4):e34206). Antibodies that detect JAM-B, JAM-C, Claudin 3, and Claudin 5 may be purchased from LifeSpan Biosciences (www.lsbio.com).

One subpopulation of co-cultured cBOECs can be prepared and segregated early (before ˜4 passages of outgrowth). Later segregation of the subpopulation can occur after ˜10 passages. After 1 week of co-culture, two cBOECs subpopulations can be compared for expression and secretion of FVIII, and suitability for engraftment in the canine liver. Co-culturing of hepatocytes can be done with several cell types including human umbilical vein endothelial cells (HUVECs). cBOECs can be used as surrogates for HUVECS in this system. Once the repaired cBOECs (with the repaired FVIII gene) are obtained, the cells can be used to induce immune tolerance in canines with high titer-antibodies to FVIII.

Example 2 Protocol for Factor VIII Gene Repair in Humans

Obtaining a Blood Sample

A protocol for gene repair of the F8 gene in blood outgrowth endothelial cells (BOECs) is described in the following example. First, a blood sample is obtained, with 50-100 mL of patient blood samples obtained by venipuncture and collection into commercially-available, medical-grade collecting devices that contain anticoagulants reagents, following standard medical guidelines for phlebotomy. Anticoagulant reagents that are used include heparin, sodium citrate, and/or ethylenediaminetetraacetic acid (EDTA). Following blood collection, all steps proceed with standard clinical practices for aseptic technique.

Isolating Appropriate Cell Populations from Blood Sample

Procedures for isolating and growing blood outgrowth endothelial cells (BOECs) have been described in detail by Hebbel and colleagues (Lin, Y., Weisdorf, D. J., Solovey, A. & Hebbel, R. P. Origins of circulating endothelial cells and endothelial outgrowth from blood. J Clin Invest 105, 71-77 (2000)). Peripheral blood mononuclear cells (PBMCs) are purified from whole blood samples by differential centrifugation using density media-based separation reagents. Examples of such separation reagents include Histopaque-1077, Ficoll-Paque, Ficoll-Hypaque, and Percoll. From these PBMCs multiple cell populations can be isolated, including BOECs. PBMCs are resuspended in EGM-2 medium without further cell subpopulation enrichment procedures and placed into 1 well of a 6-well plate coated with type I collagen. This mixture is incubated at 37° C. in a humidified environment with 5% CO2. Culture medium is changed daily. After 24 hours, unattached cells and debris are removed by washing with medium. This procedure leaves about 20 attached endothelial cells plus 100-200 other mononuclear cells. These non-endothelial mononuclear cells die within the first 2-3 weeks of culture.

Cell Culture for Growing Target Cell Population

BOECs cells are established in culture for 4 weeks with daily medium changes but with no passaging. The first passaging occurs at 4 weeks, after approximately a 100-fold expansion. In the next step, 0.025% trypsin is used for passaging cells and tissue culture plates coated with collagen-I as substrate. Following this initial 4-week establishment of the cells in culture, the BOECs are passaged again 4 days later (day 32) and 4 days after that (day 36), after which time the cells should number 1 million cells or more.

In Vitro Gene Repair

In order to affect gene repair in BOECs, cells are transfected with 0.1-10 micrograms per million cells of each plasmid encoding left and right TALENs and 0.1-10 micrograms per million cells of the repair vehicle plasmid. Transfection is done by electroporation, liposome-mediated transfection, polycation-mediated transfection, commercially available proprietary reagents for transfection, or other transfection methods using standard protocols. Following transfection, BOECs are cultured as described above for three days.

Selection of Gene-Repaired Clones

Using the method of limiting serial dilution, the BOECs are dispensed into clonal subcultures, and grown as described above. Cells are examined daily to determine which subcultures contain single clones. Upon growth of the subcultures to a density of >100 cells per subculture, the cells are trypsinized, re-suspended in medium, and a 1/10 volume of the cells is used for colony PCR. The remaining 9/10 of the cells are returned to culture. Using primers that detect productively repaired F8 genes, each 1/10 volume of colonies are screened by PCR for productive gene repair. Colonies that exhibit productive gene repair are further cultured to increase cell numbers. Using the top 20 predicted potential off-site targets of the TALENs, each of the colonies selected for further culturing is screened for possible deleterious off-site mutations. The colonies exhibiting the least number of off-site mutations are chosen for further culturing.

Preparation of Cells for Re-Introduction into Patients by Conditioning and/or Outgrowth

Prior to re-introducing the cells into patients, the BOECs are grown in culture to increase the cell numbers. In addition to continuing cell culture in the manner described above, other methods can be used to condition the cells to increase the likelihood of successful engraftment of the BOECs in the liver sinusoidal bed of the recipient patient. These other methods include: 1) co-culturing the BOECs in direct contact with hepatocytes, wherein the hepatocytes are either autologous patient-derived cells, or cells from another donor; 2) co-culturing the BOECs in conditioned medium taken from separate cultures of hepatocytes, wherein the hepatocytes that yield this conditioned medium are either autologous patient-derived cells, or cells from another donor; or 3) culturing the BOECs as spheroids in the absence of other cell types.

Co-culturing endothelial cells with hepatocytes is described further in the primary scientific literature (e.g. Kim, Y. & Rajagopalan, P. 3D hepatic cultures simultaneously maintain primary hepatocyte and liver sinusoidal endothelial cell phenotypes. PLoS ONE 5, e15456 (2010)). Culturing endothelial cells as spheroids is also described in the scientific literature (e.g. Korff, T. & Augustin, H. G. Tensional forces in fibrillar extracellular matrices control directional capillary sprouting. J Cell Sci 112 (Pt 19), 3249-3258 (1999)). Upon growing the colonies of cells to a total cell number of at least 1 billion cells, the number of cells needed for injection (>50 million cells) into the patient are separated from the remainder of the cells and used in the following step for injection into patients. The remainder of the cells are aliqouted and banked using standard cell banking procedures.

Injection of Gene-Repaired BOECs into Patients

BOECs that have been chosen for injection into patients are resuspended in sterile saline at a dose and concentration that is appropriate for the weight and age of the patient. Injection of the cell sample is performed in either the portal vein or other intravenous route of the patient, using standard clinical practices for intravenous injection.

Throughout this application, various publications are referenced. The disclosures of these publications in their entireties are hereby incorporated by reference into this application, to the extent allowed by law.

A number of aspects have been described. Nevertheless, it will be understood that various modifications may be made. Furthermore, when one characteristic or step is described it can be combined with any other characteristic or step herein even if the combination is not explicitly stated. Accordingly, other aspects are within the scope of the claims. 

1. A method of treating hemophilia A in a subject comprising: introducing into a cell of the subject one or more isolated nucleic acids encoding a nuclease that targets a portion of the F8 gene containing a mutation that causes hemophilia A, wherein the nuclease creates a double stranded break in the F8 gene; and an isolated nucleic acid comprising a donor sequence comprising (i) a nucleic acid encoding a truncated FVIII polypeptide or (ii) a native F8 3′ splice acceptor site operably linked to a nucleic acid encoding a truncated FVIII polypeptide, wherein the nucleic acid comprising the (i) nucleic acid encoding a truncated FVIII polypeptide or (ii) native F8 3′ splice acceptor site operably linked to a nucleic acid encoding a truncated FVIII polypeptide is flanked by nucleic acid sequences homologous to the nucleic acid sequences upstream and downstream of the double stranded break in the DNA, and wherein the resultant repaired gene, upon expression, confers improved coagulation functionality to the encoded FVIII protein of the subject compared to the non-repaired F8 gene.
 2. A method of inducing immune tolerance to a FVIII replacement product ((r)FVIII) in a subject having a FVIII deficiency and who will be administered, is being administered, or has been administered a (r)FVIII product comprising: introducing into a cell of the subject one or more nucleic acids encoding a nuclease that targets a portion of the F8 gene containing a mutation that causes hemophilia A, wherein the nuclease creates a double stranded break in the F8 gene; and an isolated nucleic acid comprising a donor sequence comprising (i) a nucleic acid encoding a truncated FVIII polypeptide or (ii) a native F8 3′ splice acceptor site operably linked to a nucleic acid encoding a truncated FVIII polypeptide, wherein the nucleic acid comprising the (i) nucleic acid encoding a truncated FVIII polypeptide or (ii) native F8 3′ splice acceptor site operably linked to a nucleic acid encoding a truncated FVIII polypeptide is flanked by nucleic acid sequences homologous to the nucleic acid sequences upstream and downstream of the double stranded break in the DNA, and wherein the repaired gene, upon expression, provides for the induction of immune tolerance to an administered replacement FVIII protein product.
 3. The method of claim 1, wherein the isolated nucleic acids are administered directly to the subject so that introduction into the subject's cells occurs in vivo.
 4. The method of claim 3, wherein the isolated nucleic acids can be delivered through viral transduction.
 5. The method of claim 1, wherein the isolated nucleic acids are administered ex vivo to cells that have been isolated from the subject.
 6. The method of claim 1, wherein the nucleic acids are targeted to the liver of the subject.
 7. The method of claim 1, wherein the nucleic acids are in vectors.
 8. The method of claim 1, wherein the nuclease is a zinc finger nuclease (ZFN), Transcription Activator-Like Effector Nuclease (TALEN), or a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-associated (Cas) nuclease.
 9. The method of claim 1, wherein the nuclease targets intron 22 of the F8 gene.
 10. The method of claim 1, wherein the nuclease targets intron 1 of the F8 gene.
 11. The method of claim 1, wherein the nuclease targets the exon 22/intron 22 junction.
 12. The method of claim 1, wherein the nuclease targets the exon 1/intron 1 junction.
 13. The method of claim 1, wherein the subject's F8 mutation is an intron 22 inversion.
 14. The method of claim 1, wherein the subject's F8 mutation is a point mutation or a deletion.
 15. The method of claim 1, wherein the cells are endothelial cells, hepatocytes, or stem cells.
 16. The method of claim 1, wherein the cells are blood outgrowth endothelial cells (BOECs), liver sinusoidal endothelial cells (LSECs), or induced pluripotent stem cells (iPSCs).
 17. The method of claim 16, wherein the blood outgrowth endothelial cells (BOECs) have been co-cultured with hepatocytes or liver sinusoidal endothelial cell (LSECs), or both.
 18. The method of claim 16, wherein the blood outgrowth endothelial cells (BOECs) have been co-cultured with induced pluripotent stem cells (iPSCs).
 19. An isolated nucleic acid encoding a truncated Factor VIII polypeptide consisting essentially of the amino acid sequence encoded by exons 23, 24, 25 and 26 of human Factor VIII. 20.-34. (canceled) 